What's new and what's next in diffusion MRI preprocessing

Diffusion MRI (dMRI) provides invaluable information for the study of tissue microstructure and brain connectivity, but suffers from a range of imaging artifacts that greatly challenge the analysis of results and their interpretability if not appropriately accounted for. This review will cover dMRI artifacts and preprocessing steps, some of which have not typically been considered in existing pipelines or reviews, or have only gained attention in recent years: brain/skull extraction, B-matrix incompatibilities w.r.t the imaging data, signal drift, Gibbs ringing, noise distribution bias, denoising, between- and within-volumes motion, eddy currents, outliers, susceptibility distortions, EPI Nyquist ghosts, gradient deviations, bias fields, and spatial normalization. The focus will be on “what’s new” since the notable advances prior to and brought by the Human Connectome Project (HCP), as presented in the predecessing issue on “Mapping the Connectome” in 2013. In addition to the development of novel strategies for dMRI preprocessing, exciting progress has been made in the availability of open source tools and reproducible pipelines, databases and simulation tools for the evaluation of preprocessing steps, and automated quality control frameworks, amongst others. Finally, this review will consider practical considerations and our view on “what’s next” in dMRI preprocessing

Robust processing of diffusion weighted image data

The work presented in this thesis comprises a proposed robust diffusion weighted magnetic resonance imaging (DW-MRI) pipeline, each chapter detailing a step designed to ultimately transform raw DW-MRI data into segmented bundles of coherent fibre ready for more complex analysis or manipulation. In addition to this pipeline we will also demonstrate, where appropriate, ways in which each step could be optimized for the maxillofacial region, setting the groundwork for a wider maxillofacial modelling project intended to aid surgical planning. Our contribution begins with RESDORE, an algorithm designed to automatically identify corrupt DW-MRI signal elements. While slower than the closest alternative, RESDORE is also far more robust to localised changes in SNR and pervasive image corruptions. The second step in the pipeline concerns the retrieval of accurate fibre orientation distribution functions (fODFs) from the DW-MRI signal. Chapter 4 comprises a simulation study exploring the application of spherical deconvolution methods to `generic' fibre; finding that the commonly used constrained spherical harmonic deconvolution (CSHD) is extremely sensitive to calibration but, if handled correctly, might be able to resolve muscle fODFs in vivo. Building upon this information, Chapter 5 conducts further simulations and in vivo image experimentation demonstrating that this is indeed the case, allowing us to demonstrate, for the first time, anatomically plausible reconstructions of several maxillofacial muscles. To complete the proposed pipeline, Chapter 6 then introduces a method for segmenting whole volume streamline tractographies into anatomically valid bundles. In addition to providing an accurate segmentation, this shape-based method does not require computationally expensive inter-streamline comparisons employed by other approaches, allowing the algorithm to scale linearly with respect to the number of streamlines within the dataset. This is not often true for comparison based methods which in the best case scale in higher linear time but more often by O(N2) complexity

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

Translation of Novel Imaging Techniques into Clinical Use for Patients with Epilepsy

Temporal lobe epilepsy is the most common focal epilepsy. Up to 40% of patients are refractory to medication. Anterior temporal lobe resection (ATLR) is an effective treatment but damage to the optic radiation can result in a visual field deficit (VFD) that precludes driving, a key goal of surgery. Diffusion tensor imaging tractography allows the in vivo delineation of white matter tracts such as the optic radiation. This thesis addresses the role of optic radiation tractography in planning and subsequently improving the safety of epilepsy surgery. I show how tractography assists risk stratification and surgical planning in patients with lesions near the optic radiation and assess the utility of different tractography methods for surgical planning. To derive the greatest benefit, tractography information should be available during surgery which requires correction for intraoperative brain shift and other sources of image distortion. I apply software developed at UCL in a clinical population underlying ATLR to show that postoperative imaging can predict the VFD and then use this software in real time during surgery in an intraoperative MRI suite. Updated anatomical scans can be acquired during surgery and tractography data accurately mapped on to these and displayed on the operating microscope display. I demonstrate that this image guidance allows the neurosurgeon to avoid significant VFD without affecting the seizure outcome. Diffusion imaging can also probe tissue microstructure. I explore how structural changes within the frontoparietal working memory network and temporal lobes are related to working memory impairment in TLE. I describe the structural changes that occur following ATLR showing both Wallerian degeneration and structural plasticity. Finally, I show how a novel diffusion model (NODDI) could aid the clinical assessment of patients with focal cortical dysplasia. The emphasis throughout this thesis is how diffusion imaging can be clinically useful and address clinically relevant outcomes

A Better Looking Brain: Image Pre-Processing Approaches for fMRI Data

Researchers in the field of functional neuroimaging have faced a long standing problem in pre-processing low spatial resolution data without losing meaningful details within. Commonly, the brain function is recorded by a technique known as echo-planar imaging that represents the measure of blood flow (BOLD signal) through a particular location in the brain as an array of intensity values changing over time. This approach to record a movie of blood flow in the brain is known as fMRI. The neural activity is then studied from the temporal correlation patterns existing within the fMRI time series. However, the resulting images are noisy and contain low spatial detail, thus making it imperative to pre-process them appropriately to derive meaningful activation patterns. Two of the several standard preprocessing steps employed just before the analysis stage are denoising and normalization. Fundamentally, it is difficult to perfectly remove noise from an image without making assumptions about signal and noise distributions. A convenient and commonly used alternative is to smooth the image with a Gaussian filter, but this method suffers from various obvious drawbacks, primarily loss of spatial detail. A greater challenge arises when we attempt to derive average activation patterns from fMRI images acquired from a group of individuals. The brain of one individual differs from others in a structural sense as well as in a functional sense. Commonly, the inter-individual differences in anatomical structures are compensated for by co-registering each subject\u27s data to a common normalization space, known as spatial normalization. However, there are no existing methods to compensate for the differences in functional organization of the brain. This work presents first steps towards data-driven robust algorithms for fMRI image denoising and multi-subject image normalization by utilizing inherent information within fMRI data. In addition, a new validation approach based on spatial shape of the activation regions is presented to quantify the effects of preprocessing and also as a tool to record the differences in activation patterns between individual subjects or within two groups such as healthy controls and patients with mental illness. Qualititative and quantitative results of the proposed framework compare favorably against existing and widely used model-driven approaches such as Gaussian smoothing and structure-based spatial normalization. This work is intended to provide neuroscience researchers tools to derive more meaningful activation patterns to accurately identify imaging biomarkers for various neurodevelopmental diseases and also maximize the specificity of a diagnosis

brainlife.io: A decentralized and open source cloud platform to support neuroscience research

Neuroscience research has expanded dramatically over the past 30 years by advancing standardization and tool development to support rigor and transparency. Consequently, the complexity of the data pipeline has also increased, hindering access to FAIR data analysis to portions of the worldwide research community. brainlife.io was developed to reduce these burdens and democratize modern neuroscience research across institutions and career levels. Using community software and hardware infrastructure, the platform provides open-source data standardization, management, visualization, and processing and simplifies the data pipeline. brainlife.io automatically tracks the provenance history of thousands of data objects, supporting simplicity, efficiency, and transparency in neuroscience research. Here brainlife.io's technology and data services are described and evaluated for validity, reliability, reproducibility, replicability, and scientific utility. Using data from 4 modalities and 3,200 participants, we demonstrate that brainlife.io's services produce outputs that adhere to best practices in modern neuroscience research