DEVELOPMENT OF MRI TECHNIQUES FOR MEASURING CEREBRAL BLOOD VOLUME, BLOOD FLOW, AND BLOOD OXYGENATION WITHIN A SINGLE SCAN

Functional MRI (fMRI) is commonly performed using the blood-oxygenation-level-dependent (BOLD) approach, which is sensitive to ensemble changes in cerebral blood volume (CBV), cerebral blood flow (CBF), and cerebral metabolic rate of oxygen (CMRO2). In order to understand and quantify the BOLD fMRI signal, it is essential to design multi-modal fMRI approaches that are sensitized to these individual hemodynamic parameters, and to further determine the oxygen metabolism. This dissertation aims to develop and improve current quantitative fMRI techniques to detect relaxation times T2*, cerebral blood volume (CBV), cerebral blood flow (CBF), blood oxygenation level hemodynamics, oxygen extraction fraction (OEF), and CMRO2 during neuronal activation in a time efficient manner. Total and extravascular R2* values in the parenchyma in human visual cortex are measured by combining multi-echo BOLD and vascular-space-occupancy (VASO) fMRI with visual stimulation at 7T. The VASO method is expected to suppress the intravascular signals in the microvessels. Both the absolute parenchymal extravascular R2* and R2* changes (ΔR2*) upon activation are determined, and the ratio of extravascular ΔR2* to total ΔR2* is calculated, confirming a predominant contribution from the extravascular component of the BOLD effect at 7T. Parenchymal OEF during stimulation is also estimated based on these measurements, the value of which is consistent with those reported at lower field strengths. While normally in most of the quantitative fMRI approaches, BOLD, CBV, and CBF measurements are separately performed to estimate CMRO2 dynamics, the ability to acquire these physiological parameters simultaneously would be very useful to improve image acquisition efficiency, and more importantly reduce the sensitivity to temporal variations due to factors such as subject head motion, task performance, and physiologic fluctuations between the fMRI experiments. A large portion of this dissertation is devoted to design single-scan approaches to detect changes in the multi-modal hemodynamic signals. First, a novel 3D whole-brain MRI pulse sequence, dubbed 3D VASO-FAIR, is proposed to detect CBV and CBF responses in a single scan. Second, a new 3D acquisition strategy that extends VASO-FAIR and incorporates a 3D T2-preparation gradient-echo (GRE) BOLD method is implemented to simultaneously measure BOLD, CBV, and CBF reactivity during functional stimulation. Compared to individually performed multi-modal fMRI scans, similar image quality, activation patterns, relative signal changes (ΔS/S), tSNRs and CNRs can be achieved using the proposed combined sequences. Finally, based on the BOLD, CBV, and CBF responses obtained from the combined sequence, the oxygen metabolism alterations (OEF and CMRO2) are quantified

Arterial cerebral blood volume–weighted functional MRI using pseudocontinuous arterial spin tagging (AVAST)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110725/1/mrm25220.pd

Applicability of Quantitative Functional MRI Techniques for Studies of Brain Function at Ultra-High Magnetic Field

This thesis describes the development, implementation and application of various quantitative functional magnetic resonance imaging (fMRI) approaches at ultra-high magnetic field including the assessment with regards to applicability and reproducibility. Functional MRI (fMRI) commonly uses the blood oxygenation level dependent (BOLD) contrast to detect functionally induced changes in the oxy-deoxyhaemoglobin composition of blood which reflect cerebral neural activity. As these blood oxygenation changes do not only occur at the activation site but also downstream in the draining veins, the spatial specificity of the BOLD signal is limited. Therefore, the focus has moved towards more quantitative fMRI approaches such as arterial spin labelling (ASL), vascular space occupancy (VASO) or calibrated fMRI which measure quantifiable physiologically and physically relevant parameters such as cerebral blood flow (CBF), cerebral blood volume (CBV) or cerebral metabolic rate of oxygen (CMRO2), respectively. In this thesis a novel MRI technique was introduced which allowed the simultaneous acquisition of multiple physiological parameters in order to beneficially utilise their spatial and temporal characteristics. The advantages of ultra-high magnetic field were utilised to achieve higher signal-to-noise and contrast-to-noise ratios compared to lower field strengths. This technique was successfully used to study the spatial and temporal characteristics of CBV, CBF and BOLD in the visual cortex. This technique is the first one that allows simultaneous acquisition of CBV, CBF and BOLD weighted fMRI signals in the human brain at 7 Tesla. Additionally, this thesis presented a calibrated fMRI technique which allowed the quantitative estimation of changes in cerebral oxygen metabolism at ultra-high field. CMRO2 reflects the amount of thermodynamic work due to neural activity and is therefore a significant physical measure in neuroscience. The calibrated fMRI approach presented in this thesis was optimised for the use at ultra-high field by adjusting the MRI parameters as well as implementing a specifically designed radio-frequency (RF) pulse. A biophysical model was used to calibrate the fMRI data based on the simultaneous acquisition of BOLD and CBF weighted MRI signals during a gas-breathing challenge. The reproducibility was assessed across multiple brain regions and compared to that of various physiologically relevant parameters. The results indicate that the degree of intra-subject variation for calibrated fMRI is lower than for the classic BOLD contrast or ASL. Consequently, calibrated fMRI is a viable alternative to classic fMRI contrasts with regards to spatial specificity as well as functional reproducibility. This calibrated fMRI approach was also compared to a novel direct calibration technique which relies on complete venous oxygenation saturation during the calibration scan via a gas-breathing challenge. This thesis introduced several reliable quantitative fMRI approaches at 7 Tesla and the results presented are a step forward to the wider application of quantitative fMRI.:1 Introduction 3 2 Background to Functional Magnetic Resonance Imaging 7 2.1 Magnetic Resonance 7 2.1.1 Quantum Mechanics 7 2.1.2 The Classical Point of View 10 2.1.3 Radio Frequency Pulses 12 2.1.4 Relaxation Effects 13 2.1.5 The Bloch Equations 15 2.2 Magnetic Resonance Imaging 16 2.2.1 Data Acquisition 16 2.2.2 Image Formation 17 2.2.2.1 Slice Selection 17 2.2.2.2 Frequency Encoding 18 2.2.2.3 Phase Encoding 19 2.2.2.4 Mathematics of Image Formation 20 2.2.2.5 Signal Formation 22 2.3 Advanced Imaging Methods 24 2.3.1 Echo-Planar Imaging (EPI) 24 2.3.2 Partial Fourier Acquisition 25 2.3.3 Generalised Autocalibrating Partially Parallel Acquisition (GRAPPA) 25 2.3.4 Inversion Recovery (IR) 26 2.3.5 Adiabatic Inversion 26 2.3.5.1 Hyperbolic Secant (HS) RF pulses 28 2.3.5.2 Time Resampled Frequency Offset Corrected Inversion (tr-FOCI) RF Pulses 28 2.4 Physiological Background 29 2.4.1 Neuronal Activity 30 2.4.2 Energy Metabolism 31 2.4.3 Physiological Changes During Brain Activation 32 2.4.4 The BOLD Contrast 34 2.4.5 Disadvantages of the BOLD Contrast 35 2.5 Arterial Spin Labelling (ASL) 35 2.5.1 Pulsed Arterial Spin Labelling 37 2.5.2 Arterial Spin Labelling at Ultra-High Field 41 2.6 Vascular Space Occupancy (VASO) 42 2.6.1 VASO at Ultra-High Field 44 2.6.2 Slice-Saturation Slab-Inversion (SS-SI) VASO 45 2.7 Calibrated Functional Magnetic Resonance Imaging 47 2.7.1 The Davis Model 47 2.7.2 The Chiarelli Model 50 2.7.3 The Generalised Calibration Model (GCM) 52 3 Materials and Methods 53 3.1 Scanner Setup 53 3.2 Gas Delivery and Physiological Monitoring System 53 3.3 MRI Sequence Developments 55 3.3.1 Tr-FOCI Adiabatic Inversion 55 3.3.2 Optimisation of the PASL FAIR QUIPSSII Sequence Parameters 60 3.3.3 Multi-TE Multi-TI EPI 64 4 Experiment I: Comparison of Direct and Modelled fMRI Calibration 68 4.1 Background Information 68 4.2 Methods 69 4.2.1 Experimental Design 69 4.2.2 Visuo-Motor Task 70 4.2.3 Gas Manipulations 71 4.2.4 Scanning Parameters 71 4.2.5 Data Analysis 72 4.2.6 M-value Modelling 72 4.2.7 Direct M-Value Estimation 73 4.3 Results 74 4.4 Discussion 79 4.4.1 M-value Estimation 79 4.4.2 BOLD Time Courses 82 4.4.3 M-Maps and Single Subject Analysis 82 4.4.4 Effects on CMRO2 Estimation 83 4.4.5 Technical Limitations and Implications for Calibrated fMRI 84 4.5 Conclusion 89 5 Experiment II: Reproducibility of BOLD, ASL and Calibrated fMRI 90 5.1 Background Information 90 5.2 Methods 91 5.2.1 Experimental Design 91 5.2.2 Data Analysis 91 5.2.3 Reproducibility 93 5.2.4 Learning and Habituation Effects 95 5.3 Results 95 5.4 Discussion 101 5.4.1 Breathing Manipulations 102 5.4.2 Functional Reproducibility 107 5.4.3 Habituation Effects on Reproducibility 109 5.4.4 Technical Considerations for Calibrated fMRI 110 5.5 Conclusion 112 6 Experiment III: Simultaneous Acquisition of BOLD, ASL and VASO Signals 113 6.1 Background Information 113 6.2 Methods 114 6.2.1 SS-SI VASO Signal Acquisition 114 6.2.2 ASL and BOLD Signal Acquisition 114 6.2.3 Experimental Design 114 6.2.4 Data Analysis 115 6.3 Results 115 6.4 Discussion 116 6.5 Conclusion 120 7 Conclusion and Outlook 12

Quantifying the Microvascular Origin of BOLD-fMRI from First Principles with Two-Photon Microscopy and an Oxygen-Sensitive Nanoprobe

The blood oxygenation level-dependent (BOLD) contrast is widely used in functional magnetic resonance imaging (fMRI) studies aimed at investigating neuronal activity. However, the BOLD signal reflects changes in blood volume and oxygenation rather than neuronal activity per se. Therefore, understanding the transformation of microscopic vascular behavior into macroscopic BOLD signals is at the foundation of physiologically informed noninvasive neuroimaging. Here, we use oxygen-sensitive two-photon microscopy to measure the BOLD-relevant microvascular physiology occurring within a typical rodent fMRI voxel and predict the BOLD signal from first principles using those measurements. The predictive power of the approach is illustrated by quantifying variations in the BOLD signal induced by the morphological folding of the human cortex. This framework is then used to quantify the contribution of individual vascular compartments and other factors to the BOLD signal for different magnet strengths and pulse sequences.National Institutes of Health (U.S.) (Grant P41RR14075)National Institutes of Health (U.S.) (Grant R01NS067050)National Institutes of Health (U.S.) (Grant R01NS057198)National Institutes of Health (U.S.) (Grant R01EB000790)American Heart Association (Grant 11SDG7600037)Advanced Multimodal NeuroImaging Training Program (R90DA023427

Cortical depth dependent functional responses in humans at 7T: improved specificity with 3D GRASE

Ultra high fields (7T and above) allow functional imaging with high contrast-to-noise ratios and improved spatial resolution. This, along with improved hardware and imaging techniques, allow investigating columnar and laminar functional responses. Using gradient-echo (GE) (T2* weighted) based sequences, layer specific responses have been recorded from human (and animal) primary visual areas. However, their increased sensitivity to large surface veins potentially clouds detecting and interpreting layer specific responses. Conversely, spin-echo (SE) (T2 weighted) sequences are less sensitive to large veins and have been used to map cortical columns in humans. T2 weighted 3D GRASE with inner volume selection provides high isotropic resolution over extended volumes, overcoming some of the many technical limitations of conventional 2D SE-EPI, whereby making layer specific investigations feasible. Further, the demonstration of columnar level specificity with 3D GRASE, despite contributions from both stimulated echoes and conventional T2 contrast, has made it an attractive alternative over 2D SE-EPI. Here, we assess the spatial specificity of cortical depth dependent 3D GRASE functional responses in human V1 and hMT by comparing it to GE responses. In doing so we demonstrate that 3D GRASE is less sensitive to contributions from large veins in superficial layers, while showing increased specificity (functional tuning) throughout the cortex compared to GE

Functional Imaging of Autonomic Regulation: Methods and Key Findings.

Central nervous system processing of autonomic function involves a network of regions throughout the brain which can be visualized and measured with neuroimaging techniques, notably functional magnetic resonance imaging (fMRI). The development of fMRI procedures has both confirmed and extended earlier findings from animal models, and human stroke and lesion studies. Assessments with fMRI can elucidate interactions between different central sites in regulating normal autonomic patterning, and demonstrate how disturbed systems can interact to produce aberrant regulation during autonomic challenges. Understanding autonomic dysfunction in various illnesses reveals mechanisms that potentially lead to interventions in the impairments. The objectives here are to: (1) describe the fMRI neuroimaging methodology for assessment of autonomic neural control, (2) outline the widespread, lateralized distribution of function in autonomic sites in the normal brain which includes structures from the neocortex through the medulla and cerebellum, (3) illustrate the importance of the time course of neural changes when coordinating responses, and how those patterns are impacted in conditions of sleep-disordered breathing, and (4) highlight opportunities for future research studies with emerging methodologies. Methodological considerations specific to autonomic testing include timing of challenges relative to the underlying fMRI signal, spatial resolution sufficient to identify autonomic brainstem nuclei, blood pressure, and blood oxygenation influences on the fMRI signal, and the sustained timing, often measured in minutes of challenge periods and recovery. Key findings include the lateralized nature of autonomic organization, which is reminiscent of asymmetric motor, sensory, and language pathways. Testing brain function during autonomic challenges demonstrate closely-integrated timing of responses in connected brain areas during autonomic challenges, and the involvement with brain regions mediating postural and motoric actions, including respiration, and cardiac output. The study of pathological processes associated with autonomic disruption shows susceptibilities of different brain structures to altered timing of neural function, notably in sleep disordered breathing, such as obstructive sleep apnea and congenital central hypoventilation syndrome. The cerebellum, in particular, serves coordination roles for vestibular stimuli and blood pressure changes, and shows both injury and substantially altered timing of responses to pressor challenges in sleep-disordered breathing conditions. The insights into central autonomic processing provided by neuroimaging have assisted understanding of such regulation, and may lead to new treatment options for conditions with disrupted autonomic function

NONINVASIVE IMAGING OF BRAIN VASCULATURE WITH HIGH RESOLUTION BLOOD OXYGENATION LEVEL-DEPENDENT VENOGRAPHY IN MAGNETIC RESONANCE IMAGING: APPLICATIONS TO FUNCTIONAL AND CLINICAL STUDIES

BOLD techniques have been used in a vast range of applications including functional MRI (fMRI) and clinical MR venography of brain vasculature. Despite the immense success of BOLD fMRI applications, our understanding of complex neuronal and hemodynamic processes associated with BOLD techniques is limited. An experimental investigation with BOLD MR venography may allow us to expand our knowledge in hemodynamic process involved in BOLD fMRI. BOLD techniques are also clinically useful. In clinical brain imaging studies, imaging both time-of-flight (TOF) MR angiogram (MRA) and BOLD MR venogram (MRV) is often desirable, because they complement the depiction of vascular pathologies. Nevertheless, MRV is usually not acquired to minimize the image acquisition time. It will be highly beneficial if we can acquire MRV while imaging MRA without increasing scan time. Thus, the objective of our study was to develop and assess BOLD MRV techniques for both functional and clinical applications. For the experimental evaluation of BOLD MRV, we used a rat brain model at 9.4T. The scan condition for BOLD MRV was optimized and the venous origin of hypointense vasculature was investigated with modulation of oxygenation. Detailed venules of ˜16-30μm diameter were detected in the resulting in vivo images with 78μm isotropic scan resolution, verified with in vivo two-photon microscopy and computer simulation data. Activation foci of high-resolution BOLD fMRI maps were correlated with relatively large intracortical veins detected with high-resolution BOLD MRV, indicating that detectability of conventional BOLD fMRI is limited by density of these intracortical veins (˜1.5 vessels/mm²). For the clinical application of BOLD MRV, we developed and tested a compatible dual-echo arteriovenography (CODEA) technique for simultaneous acquisition of TOF MRA and BOLD MRV at a 3T human system. Image quality of the CODEA technique acquired in a single session was comparable to conventional TOF MRA and BOLD MRV separately acquired in two sessions. The CODEA technique was applied to chronic stroke studies. Detailed vascular structures including arterial occlusions and venous abnormalities were depicted. The CODEA technique appears valuable to other clinical applications, particularly for those requiring efficient MRA/MRV imaging with limited scan time such as acute stroke studies