Estimation of Fiber Orientations Using Neighborhood Information

Data from diffusion magnetic resonance imaging (dMRI) can be used to reconstruct fiber tracts, for example, in muscle and white matter. Estimation of fiber orientations (FOs) is a crucial step in the reconstruction process and these estimates can be corrupted by noise. In this paper, a new method called Fiber Orientation Reconstruction using Neighborhood Information (FORNI) is described and shown to reduce the effects of noise and improve FO estimation performance by incorporating spatial consistency. FORNI uses a fixed tensor basis to model the diffusion weighted signals, which has the advantage of providing an explicit relationship between the basis vectors and the FOs. FO spatial coherence is encouraged using weighted l1-norm regularization terms, which contain the interaction of directional information between neighbor voxels. Data fidelity is encouraged using a squared error between the observed and reconstructed diffusion weighted signals. After appropriate weighting of these competing objectives, the resulting objective function is minimized using a block coordinate descent algorithm, and a straightforward parallelization strategy is used to speed up processing. Experiments were performed on a digital crossing phantom, ex vivo tongue dMRI data, and in vivo brain dMRI data for both qualitative and quantitative evaluation. The results demonstrate that FORNI improves the quality of FO estimation over other state of the art algorithms.Comment: Journal paper accepted in Medical Image Analysis. 35 pages and 16 figure

Fast Fiber Orientation Estimation in Diffusion MRI from kq-Space Sampling and Anatomical Priors

High spatio-angular resolution diffusion MRI (dMRI) has been shown to provide accurate identification of complex fiber configurations, albeit at the cost of long acquisition times. We propose a method to recover intra-voxel fiber configurations at high spatio-angular resolution relying on a kq-space under-sampling scheme to enable accelerated acquisitions. The inverse problem for reconstruction of the fiber orientation distribution (FOD) is regularized by a structured sparsity prior promoting simultaneously voxelwise sparsity and spatial smoothness of fiber orientation. Prior knowledge of the spatial distribution of white matter, gray matter and cerebrospinal fluid is also assumed. A minimization problem is formulated and solved via a forward-backward convex optimization algorithmic structure. Simulations and real data analysis suggest that accurate FOD mapping can be achieved from severe kq-space under-sampling regimes, potentially enabling high spatio-angular dMRI in the clinical setting.Comment: 10 pages, 5 figures, Supplementary Material

Fast high spatio-angular resolution estimation of the neuronal fiber orientations in the brain with diffusion MRI

The human brain is a very complex organ. The white matter tissue composing the brain is made of threadlike structures, called axons, which are responsible for the transmission of the impulses between different areas of the brain. Axons are extremely fine and cannot be visualized by any in vivo imaging technique, leaving a lot to explore about which brain regions are connected and how information is carried through these structures. Diffusion Magnetic Resonance Imaging (dMRI) is a unique technique that allows to investigate the inner structures of the brain in vivo and in a non-invasive way. High spatio-angular resolution dMRI techniques have been shown to provide accurate fiber reconstructions even in the presence of complex fiber configurations. However, high resolution techniques are characterized by long acquisition times, which hamper their application into the clinical practice. In this manuscript we present a novel method to recover the fiber orientation distribution (FOD) of the bundles of axons at high spatio-angular resolution via practical kq-space under-sampling that enables both acceleration and super-resolution. The quality of the recovered fibers is preserved by making use of advanced anatomical priors for the FOD reconstruction. Prior knowledge of the spatial distribution of the white matter, the gray matter and the cerebrospinal fluid is taken into account for the recovery of the FOD coefficients. In addition, the simultaneous voxelwise sparsity and spatial smoothness of fiber orientations is accounted for by means of a structured sparsity prior. A convex minimization problem is formulated and solved via an accelerated stochastic Forward-Backward algorithm. Simulations show that the proposed method outperforms state-of-the-art kq-space approaches in terms of reconstruction quality. Real data analysis suggests that accurate FOD mapping can be achieved from severe kq-space under-sampling regimes, potentially enabling the application of high spatio-angular resolution dMRI into the clinical practice

Chapter 7 Estimating chemical and microstructural heterogeneity by correlating relaxation and diffusion

Whereas diffusion NMR can probe the structural configurations configurations of microscopic environments in biological tissue, relaxation can provide complementary information on their chemical composition. This chapter considers experiments in which diffusion diffusion and relaxation properties are sampled simultaneously by varying multiple acquisition parameters. As such, correlations between the diffusion and relaxation can be established, providing an altogether more complete picture of heterogeneous tissue

A sparse reconstruction framework for Fourier-based plane wave imaging

International audienceUltrafast imaging based on plane-wave (PW) insonification is an active area of research due to its capability of reaching high frame rates. Among PW imaging methods, Fourier-based approaches have demonstrated to be competitive compared with traditional delay and sum methods. Motivated by the success of compressed sensing techniques in other Fourier imaging modalities, like magnetic resonance imaging, we propose a new sparse regularization framework to reconstruct high-quality ultrasound (US) images. The framework takes advantage of both the ability to formulate the imaging inverse problem in the Fourier domain and the sparsity of US images in a sparsifying domain. We show, by means of simulations, in vitro and in vivo data, that the proposed framework significantly reduces image artifacts, i.e., measurement noise and sidelobes, compared with classical methods, leading to an increase of the image quality

Modelling individual variations in brain structure and function using multimodal MRI

Every brain is different. Understanding this variability is crucial for investigating the neural substrate underlying individuals’ unique behaviour and developing personalised diagnosis and treatments. This thesis presents novel computational approaches to study individual variability in brain structure and function using magnetic resonance imaging (MRI) data. It comprises three main chapters, each addressing a specific challenge in the field. In Chapter 3, the thesis proposes a novel Image Quality Transfer (IQT) technique, HQ-augmentation, to accurately localise a Deep Brain Stimulation (DBS) target in low-quality clinical-like data. Leveraging high-quality diffusion MRI datasets from the Human Connectome Project (HCP), the HQ-augmentation approach is robust to corruptions in data quality while preserving the individual anatomical variability of the DBS target. It outperforms existing alternatives and generalises to unseen low-quality diffusion MRI datasets with different acquisition protocols, such as the UK Biobank (UKB) dataset. In Chapter 4, the thesis presents a framework for enhancing prediction accuracy of individual task-fMRI activation profiles using the variability of resting-state fMRI. Assuming resting-state functional modes underlie task-evoked activity, this chapter demonstrates that shape and intensity of individualised task activations can be separately modelled. This chapter introduced the concept of "residualisation" and showed that training on residuals leads to better individualised predictions. The framework’s prediction accuracy, validated on HCP and UKB data, is on par with task-fMRI test-retest reliability, suggesting potential for supplementing traditional task localisers. In Chapter 5, the thesis presents a novel framework for individualised retinotopic mapping using resting-state fMRI, from the primary visual cortex to visual cortex area 4. The proposed approach reproduces task-elicited retinotopy and captures individual differences in retinotopic organisation. The proposed framework delineates borders of early visual areas more accurately than group-average parcellation and is effective with both high-field 7T and more common 3T resting-state fMRI data, providing a valuable alternative to resource-intensive retinotopy task-fMRI experiments. Overall, this thesis demonstrates the potential of advanced MRI analysis techniques to study individual variability in brain structure and function, paving the way for improved clinical applications tailored to individual patients and a better understanding of neural mechanisms underlying unique human behaviour

Fast diffusion MRI based on sparse acquisition and reconstruction for long-term population imaging

Diffusion weighted magnetic resonance imaging (dMRI) is a unique MRI modality to probe the diffusive molecular transport in biological tissue. Due to its noninvasiveness and its ability to investigate the living human brain at submillimeter scale, dMRI is frequently performed in clinical and biomedical research to study the brain’s complex microstructural architecture. Over the last decades large prospective cohort studies have been set up with the aim to gain new insights into the development and progression of brain diseases across the life span and to discover biomarkers for disease prediction and potentially prevention. To allow for diverse brain imaging using different MRI modalities, stringent scan time limits are typically imposed in population imaging. Nevertheless, population studies aim to apply advanced and thereby time consuming dMRI protocols that deliver high quality data with great potential for future analysis. To allow for time-efficient but also versatile diffusion imaging, this thesis contributes to the investigation of accelerating diffusion spectrum imaging (DSI), an advanced dMRI technique that acquires imaging data with high intra-voxel resolution of tissue microstructure. Combining state-of-the-art parallel imaging and the theory of compressed sensing (CS) enables the acceleration of spatial encoding and diffusion encoding in dMRI. In this way, the otherwise long acquisition times in DSI can be reduced significantly. In this thesis, first, suitable q-space sampling strategies and basis functions are explored that fulfill the requirements of CS theory for accurate sparse DSI reconstruction. Novel 3D q-space sample distributions are investigated for CS-DSI. Moreover, conventional CS-DSI based on the discrete Fourier transform is compared for the first time to CS-DSI based on the continuous SHORE (simple harmonic oscillator based reconstruction and estimation) basis functions. Based on these findings, a CS-DSI protocol is proposed for application in a prospective cohort study, the Rhineland Study. A pilot study was designed and conducted to evaluate the CS-DSI protocol in comparison with state-of-the-art 3-shell dMRI and dedicated protocols for diffusion tensor imaging (DTI) and for the combined hindered and restricted model of diffusion (CHARMED). Population imaging requires processing techniques preferably with low computational cost to process and analyze the acquired big data within a reasonable time frame. Therefore, a pipeline for automated processing of CS-DSI acquisitions was implemented including both in-house developed and existing state-of-the-art processing tools. The last contribution of this thesis is a novel method for automatic detection and imputation of signal dropout due to fast bulk motion during the diffusion encoding in dMRI. Subject motion is a common source of artifacts, especially when conducting clinical or population studies with children, the elderly or patients. Related artifacts degrade image quality and adversely affect data analysis. It is, thus, highly desired to detect and then exclude or potentially impute defective measurements prior to dMRI analysis. Our proposed method applies dMRI signal modeling in the SHORE basis and determines outliers based on the weighted model residuals. Signal imputation reconstructs corrupted and therefore discarded measurements from the sparse set of inliers. This approach allows for fast and robust correction of imaging artifacts in dMRI which is essential to estimate accurate and precise model parameters that reflect the diffusive transport of water molecules and the underlying microstructural environment in brain tissue.Die diffusionsgewichtete Magnetresonanztomographie (dMRT) ist ein einzigartiges MRTBildgebungsverfahren, um die Diffusionsbewegung von Wassermolekülen in biologischem Gewebe zu messen. Aufgrund der Möglichkeit Schichtbilder nicht invasiv aufzunehmen und das lebende menschliche Gehirn im Submillimeter-Bereich zu untersuchen, ist die dMRT ein häufig verwendetes Bildgebungsverfahren in klinischen und biomedizinischen Studien zur Erforschung der komplexen mikrostrukturellen Architektur des Gehirns. In den letzten Jahrzehnten wurden große prospektive Kohortenstudien angelegt, um neue Einblicke in die Entwicklung und den Verlauf von Gehirnkrankheiten über die Lebenspanne zu erhalten und um Biomarker zur Krankheitserkennung und -vorbeugung zu bestimmen. Um durch die Verwendung unterschiedlicher MRT-Verfahren verschiedenartige Schichtbildaufnahmen des Gehirns zu ermöglich, müssen Scanzeiten typischerweise stark begrenzt werden. Dennoch streben Populationsstudien die Anwendung von fortschrittlichen und daher zeitintensiven dMRT-Protokollen an, um Bilddaten in hoher Qualität und mit großem Potential für zukünftige Analysen zu akquirieren. Um eine zeiteffizente und gleichzeitig vielseitige Diffusionsbildgebung zu ermöglichen, leistet diese Dissertation Beiträge zur Untersuchung von Beschleunigungsverfahren für die Bildgebung mittels diffusion spectrum imaging (DSI). DSI ist ein fortschrittliches dMRT-Verfahren, das Bilddaten mit hoher intra-voxel Auflösung der Gewebestruktur erhebt. Werden modernste Verfahren zur parallelen MRT-Bildgebung mit der compressed sensing (CS) Theorie kombiniert, ermöglicht dies eine Beschleunigung der räumliche Kodierung und der Diffusionskodierung in der dMRT. Dadurch können die ansonsten langen Aufnahmezeiten für DSI erheblich reduziert werden. In dieser Arbeit werden zuerst geeigenete Strategien zur Abtastung des q-space sowie Basisfunktionen untersucht, welche die Anforderungen der CS-Theorie für eine korrekte Signalrekonstruktion der dünnbesetzten DSI-Daten erfüllen. Neue 3D-Verteilungen von Messpunkten im q-space werden für die Verwendung in CS-DSI untersucht. Außerdem wird konventionell auf der diskreten Fourier-Transformation basierendes CS-DSI zum ersten Mal mit einem CS-DSI Verfahren verglichen, welches kontinuierliche SHORE (simple harmonic oscillator based reconstruction and estimation) Basisfunktionen verwendet. Aufbauend auf diesen Ergebnissen wird ein CS-DSI-Protokoll zur Anwendung in einer prospektiven Kohortenstudie, der Rheinland Studie, vorgestellt. Eine Pilotstudie wurde entworfen und durchgeführt, um das CS-DSI-Protokoll im Vergleich mit modernster 3-shell-dMRT und mit dedizierten Protokollen für diffusion tensor imaging (DTI) und für das combined hindered and restricted model of diffusion (CHARMED) zu evaluieren. Populationsbildgebung erfordert Prozessierungsverfahren mit möglichst geringem Rechenaufwand, um große akquirierte Datenmengen in einem angemessenen Zeitrahmen zu verarbeiten und zu analysieren. Dafür wurde eine Pipeline zur automatisierten Verarbeitung von CS-DSI-Daten implementiert, welche sowohl eigenentwickelte als auch bereits existierende moderene Verarbeitungsprogramme enthält. Der letzte Beitrag dieser Arbeit ist eine neue Methode zur automatischen Detektion und Imputation von Signalabfall, welcher durch schnelle Bewegungen während der Diffusionskodierung in der dMRT entsteht. Bewegungen der Probanden während der dMRT-Aufnahme sind eine häufige Ursache für Bildfehler, vor allem in klinischen oder Populationsstudien mit Kindern, alten Menschen oder Patienten. Diese Artefakte vermindern die Datenqualität und haben einen negativen Einfluss auf die Datenanalyse. Daher ist es das Ziel, fehlerhafte Messungen vor der dMRI-Analyse zu erkennen und dann auszuschließen oder wenn möglich zu ersetzen. Die vorgestellte Methode verwendet die SHORE-Basis zur dMRT-Signalmodellierung und bestimmt Ausreißer mit Hilfe von gewichteten Modellresidualen. Die Datenimputation rekonstruiert die unbrauchbaren und daher verworfenen Messungen mit Hilfe der verbleibenden, dünnbesetzten Menge an Messungen. Dieser Ansatz ermöglicht eine schnelle und robuste Korrektur von Bildartefakten in der dMRT, welche erforderlich ist, um korrekte und präzise Modellparameter zu schätzen, die die Diffusionsbewegung von Wassermolekülen und die zugrundeliegende Mikrostruktur des Gehirngewebes reflektieren