The assessment of Myocardial Blood Flow (MBF) is an important measure in clinical practice for evaluating the health of the heart. Multiple imaging methods have been employed to measure MBF, including applications of nuclear medicine, x-ray and contrast enhanced Magnetic Resonance Imaging (MRI). However, each of these modalities suffers from drawbacks, such as invasiveness due to radiation or intravenous contrast injection, difficulty in quantitation, and limited repeatability. The aim of this thesis was to develop a non-invasive, quantitative and repeatable MRI method for the measurement of MBF, by applying the techniques of Arterial Spin Labelling (ASL). A novel cardiac ASL sequence was designed and thoroughly tested by simulation and phantom experiment. The method was applied in vivo in three slices of the human heart, to our knowledge the first cardiac ASL acquisition in multiple slices, in ten healthy volunteers. The resulting values of mid-ventricular MBF, averaged over multiple measurements, compared well with the literature values from multiple modalities. Repeat measures were then used in order to characterise the reproducibility and variation inherent in the method, showing that the expected change in MBF would be detectable with the ASL sequence. Segmental values of MBF, according to the AHA standard model, were also calculated and these compared well to previous PET literature. This work has been published in the journal Magnetic Resonance in Medicine. Further to this work, the new cardiac ASL sequence was optimised with the ultimate goal of single breath hold acquisitions. The optimised sequence was shown to improve the results in terms of the balance between good signal-to-noise ratio and reducing spatial and temporal variation in MBF values. Though improvements were made, there remained a large variation in the measured values of MBF, meaning single breath hold acquisition in a clinical context is not yet practical. In addition to the optimisation, the online scanner reconstruction software was altered to produce parametric maps of both T₁ and MBF direct to the scanner operator. The sequence, along with online reconstruction is available for use in our laboratory for future clinical trials in the heart and liver.

Frontotemporal lobar degeneration (FTLD) is a heterogeneous group of illnesses which can be difficult to diagnose. Modern diagnostic criteria require the presence of imaging abnormalities, but these are not always seen in the early stages of the illness. Hence there is a need to consider the use of more advanced MR techniques. This thesis reports the results of a multimodal MRI study of patients with FTLD, and considers two things: how well data from the different modalities can classify patients, and how well the different modalities can identify affected tissue. FTLD is thought to involve alterations in cerebral blood flow, but it is possible that microvascular changes will alter additional perfusion parameters, such as the time taken for blood to reach the tissue (the arrival time). Multi-time point arterial spin labelling (ASL) measurements have the ability to extract the relevant parameters. I consider the parameters involved in modelling these data, and report the accuracy of cerebral blood flow (CBF) measurement achievable in a clinically acceptable time. FTLD patients have atrophy in the frontal and temporal lobes, regions problematic for MRI because of susceptibility artefacts caused by adjacent air spaces. I consider two ASL MR read-out sequences (gradient-echo and spin-echo)and show that spin-echo images give higher signal in frontal and temporal regions than gradient-echo. ASL, T1-weighted and diffusion-weighted images were collected for a group of 17 FTLD patients and 18 controls. I found decreased CBF in highly atrophied regions of cortical grey matter in patients, but this deficit was not seen when corrected for atrophy. An increased arrival time was seen in regions adjacent to the atrophied regions, but a decreased arrival time was seen in the atrophied regions; this is a novel finding. The diffusion metrics of fractional anisotropy (FA) and particularly mean diffusivity (MD) are found to be highly sensitive to differences in FTLD patients. I speculate that this is an increased sensitivity to atrophy because of the increased signal from cerebrospinal fluid. I combine the regional values of all the modalities in a classification method to distinguish patients from controls, and establish a combination of region and modality that classified 21/22 subjects correctly. This exploratory study is the first time all three modalities have been combined in a study of FTLD patients; it shows that combining MR modalities may lead to improved classification of FTLD patients and better identification of affected tissue.

At present, there are few clinically effective pain therapies available to treat chronic pain. One reason is due to a lack of understanding about how pain emerges in the brain. Excitingly, an emerging body of work suggests that the perfusion imaging technique, arterial spin labelling (ASL), is particularly well-suited to investigate this issue. The primary aim of this thesis is to develop and optimise a quantitative perfusion imaging approach to investigate the neural correlates of both experimental and pathological tonic pain. In Chapter 2, we explore different methods of inducing ongoing pain in healthy subjects. Results from this study show that mechanically induced pain is well suited for use in ASL FMRI experiments. In Chapter 3, we compare currently available ASL FMRI approaches for investigating tonic states, using a range of sensory paradigms. Results from these experiments support the use of an optimised version of Continuous ASL (CASL) FMRI to obtain whole-brain perfusion. Additionally, we discuss our decision to proceed with the newly acquired pseudo-continuous ASL (pCASL); a novel ASL technique that benefits from maximal signal-to-noise (SNR) across a whole-brain volume. In Chapter 4 we implement the pCASL FMRI approach to image the neural correlates of ongoing experimental pain. Results from the investigation of parametrically modulated ongoing mechanical pain show robust pain-related activation of key pain related regions that are monotonically active with an increase in stimulus intensity. Additionally, data from this experiment shows the presence of complex perfusion dynamics relative to pain worthy of further study. In Chapter 5, we optimised the pCASL sequence to obtain absolute perfusion changes across the whole-brain volume, using multi-inversion times, so that we could investigate the perfusion dynamics observed in Chapter 4. Results show that absolute perfusion changes during tonic pain are considerably less than for regions recruited during a non- pain task. Additionally, dynamic perfusion changes show complex stimulus responses across all active regions regardless of stimulus type. We conclude that while the technique is well suited to quantify absolute perfusion, the mechanisms underlying the dynamic changes in CBF (neuronal signal, neurovascular coupling) need further study. Finally, in Chapter 6, we implement the absolute perfusion approach developed in Chaper 5 to interrogate the neural correlates of the genetic pain disease, Erythromelalgia, and pleasurable relief. The results of this study show pain-related activation (and relief-induced reduction) of key pain-related regions. We conclude from these results that the ASL technique developed over the course of this thesis can be used to study a range of pain pathologies. Taken together, the results of this thesis document the development of a powerful perfusion imaging technique capable of quantifying absolute perfusion changes across a whole-brain volume. The data presented here from investigations of both experimental and pathological pain states supports the use of this technique in future tonic pain studies, as well as other neuroscience applications. We are confident that implementation of this imaging approach will provide integral insight into the mechanisms of ongoing pain states; and further the development of novel efficacious pain treatment options.

Ischaemic stroke is a major cause of death and disability worldwide. Cerebral autoregulation, which can be impaired during acute stroke, and collateral flow to brain tissue through the circle of Willis, both play a role in preventing tissue infarction. The configuration of the arterial circle varies between individuals. Thus, personalised modelling of the cerebral arterial network, to determine the potential for collateral flow, can be of significant value in the clinical context of stroke. The interaction between autoregulation and collateral flow remains poorly understood. In this study, steady-state physiological models of the cerebral arterial network, including several common variants of the circle of Willis, were coupled to a spatially variable mathematical representation of cerebral autoregulation. The resulting model was used to simulate various arterial occlusions, as well as bilateral and unilateral impairment of autoregulation, in each structural variant. The work identified few circle of Willis variants that present either particularly high-risk or particularly low-risk of cerebral ischaemia. Instead it was found that most variants are dependent upon the bilateral function of autoregulation to facilitate collateral flow and preserve cerebral blood flows. When autoregulation was impaired unilaterally, downstream of an occlusion, blood flows in the contralateral hemisphere were preserved at the expense of the ipsilateral tissue at risk. Arterial network models have in the past been personalised using structural, rather than functional, angiography measurements. This thesis presents a novel model-based method for absolute blood volume flow rate quantification in short arterial segments using dynamic magnetic resonance angiography data. The work also investigated the additional information that can be obtained from such functional angiography. The flow quantification technique was found to accurately estimate flows in shorter arterial segments than an existing technique. However, improvements to noise performance, and strategies for rejection of contaminating signals from overlapping vessels within the imaging plane, are required before the technique can be applied to personalised cerebral arterial network modelling.

L’imagerie par résonance magnétique (IRM) est un outil important pour l’investigation qualitative et quantitative de la physiologie du cerveau. L’investigation de l’activité neuronale à l’aide de cette modalité est possible grâce à la détection de changements hémodynamiques qui surviennent de manière concomitante aux activités de signalisation des neurones, tels l’augmentation régionale du débit sanguin cérébral (CBF) ou encore la variation de la concentration de désoxyhémoglobine dans les vaisseaux veineux. Pour étudier la formation de contrastes fonctionnels qui découlent de ces phénomènes, deux séquences de pulses ont été développées en vue d’expériences en IRM fonctionnelle (IRMf) visant l’imagerie du signal oxygéno-dépendant BOLD ainsi que de la perfusion. Le premier objectif de cette thèse fut le développement d’une séquence de type écho-planar (EPI) permettant l’acquisition entrelacée d’images en mode échos de gradient (GRE-EPI) ainsi qu’en mode échos de spins (SE-EPI) pour l’évaluation de la performance de ces deux méthodes d’imagerie au cours d’une expérience en IRMf BOLD impliquant l’utilisation d’un stimulus visuel chez 4 sujets adultes sains. Le deuxième objectif principal de cette thèse fut le développement d’une séquence de marquage de spins artériels employant un module de marquage fonctionnant en mode pseudo-continu (pCASL) pour la quantification du CBF au repos. Cette séquence fut testée chez 3 sujets adultes en bonne santé et sa performance fut comparée à celle d’une séquence similaire développée par un groupe de recherche extérieur. Les résultats de l’expérience portant sur le contraste BOLD indiquent une supériorité de la performance du mode GRE-EPI vis-à-vis celle du mode SE-EPI en termes des valeurs moyennes du pourcentage de l’ampleur d’effet et du score t associés à l’activité neuronale en réponse au stimulus. L’expérience visant la quantification du CBF démontra la capacité de la séquence pCASL développée au cours de ce projet de calculer des valeurs de la perfusion de la matière grise ainsi que du cerveau entier se retrouvant dans une plage de valeurs qui sont physiologiquement acceptables, mais qui demeurent inférieures à celles obtenues par la séquence pCASL développée par le groupe de recherche extérieur. Des expériences futures seront effectuées pour optimiser le fonctionnement des séquences présentées dans ce mémoire en plus de quantifier l’efficacité d’inversion de la séquence pCASL. / Magnetic resonance imaging (MRI) is an important tool for the qualitative and quantitative investigation of brain physiology. The investigation of neuronal activation using this modality is made possible by the detection of concomitantly-arising hemodynamic changes in the brain’s vasculature, such as localized increases of the cerebral blood flow (CBF) or the variation of the concentration of paramagnetic deoxyhemoglobin in venous vessels. To study the formation of functional contrasts that stem from these changes in MRI, two pulse sequences were developed in this thesis to carry out experiments in blood oxygenation level dependent (BOLD) and perfusion functional MRI (fMRI). The first objective laid out in this work was the development of an echo planar imaging (EPI) sequence permitting the interleaved acquisition of images using gradient-echo EPI and spin-echo EPI to assess the performances of these imaging techniques in a BOLD fMRI experiment involving a visual stimulation paradigm in 4 healthy adult subjects. The second main objective of this thesis was the development of a pseudo-continuous arterial spin labelling (pCASL) sequence for the quantification of cerebral blood flow (CBF) at rest. This sequence was tested on 3 healthy adult subjects and compared to an externally-developed pCASL sequence to assess its performance. The results of the BOLD fMRI experiment indicated that the performance of GRE-EPI was superior to that of SE-EPI in terms of the average percent effect size and t-score associated with stimulus-driven neuronal activation. The CBF quantification experiment demonstrated the ability of the in-house pCASL sequence to compute values of CBF that are within a range of physiologically-acceptable values while remaining inferior to those computed using the externally-developed pCASL sequence. Future experiments will focus on the optimization of the sequences presented in this thesis as well as on the quantification of the pCASL sequence’s labelling efficiency.

Collateral blood flow is the compensatory flow of blood to the tissue through secondary channels when the primary channel is compromised. It is of vital importance in cerebrovascular disease where collateral flow can maintain large regions of brain tissue which would otherwise have suffered ischaemic damage. Traditional x-ray based techniques for visualising collateral flow are invasive and carry risks to the patient. In this thesis novel magnetic resonance imaging techniques for performing vessel-selective labelling of brain feeding arteries are explored and developed to reveal the source and extent of collateral flow in the brain non-invasively and without the use of contrast agents. Vessel-encoded pseudo-continuous arterial spin labelling (VEPCASL) allows the selective labelling of blood water in different combinations of brain feeding arteries that can be combined in post-processing to yield vascular territory maps. The mechanism of VEPCASL was elucidated and optimised through simulations of the Bloch equations and phantom experiments, including its sensitivity to sequence parameters, blood velocity and off-resonance effects. An implementation of the VEPCASL pulse sequence using an echo-planar imaging (EPI) readout was applied in healthy volunteers to enable optimisation of the post-labelling delay and choice of labelling plane position. Improvements to the signal-to-noise ratio (SNR) and motion-sensitivity were made through the addition of background suppression pulses and a partial-Fourier scheme. Experiments using a three-dimensional gradient and spin echo (3D-GRASE) readout were somewhat compromised by significant blurring in the slice direction, but showed potential for future work with a high SNR and reduced dropout artefacts. The VEPCASL preparation was also applied to a dynamic 2D angiographic readout, allowing direct visualisation of collateral blood flow in the brain as well as a morphological and functional assessment of the major cerebral arteries. The application of a balanced steady-state free precession (bSSFP) readout significantly increased the acquisition efficiency, allowing the generation of dynamic 3D vessel-selective angiograms. A theoretical model of the dynamic angiographic signal was also derived, allowing quantification of blood flow through specified vessels, providing a significant advantage over qualitative x-ray based methods. Finally, these methods were applied to a number of patient groups, including those with vertebro-basilar disease, carotid stenosis and arteriovenous malformation. These preliminary studies demonstrate that useful clinical information regarding collateral blood flow can be obtained with these techniques.

Cette thèse aborde l'étude de la fonction cérébrale en Imagerie par Résonance Magnétique (IRM) à l'aide de deux séquences : l'IRM fonctionnelle (IRMf) BOLD et l'imagerie de perfusion par marquage de spins (ASL). Dans ce contexte, les analyses de groupe jouent un rôle important dans l'identification des dysfonctionnements globaux associés à une pathologie. D'autre part, les études individuelles, qui fournissent des conclusions au niveau d'un sujet unique, présentent un intérêt croissant. Dans ce travail, nous abordons à la fois les études de groupe et les analyses individuelles. Dans un premier temps, nous réalisons une analyse de groupe en IRMf BOLD en vue d'étudier la dysphasie chez l'enfant, une pathologie peu explorée en neuroimagerie. Nous mettons ainsi en évidence un fonctionnement et une latéralisation atypiques des aires langagières. Ensuite, nous nous concentrons sur les analyses individuelles. Nous proposons l'utilisation d'estimateurs robustes pour calculer les cartographies de débit sanguin cérébral en ASL. Ensuite, nous étudions la validité des hypothèses qui sous-tendent les analyses statistiques standard dans le contexte de l'ASL. Finalement, nous proposons une nouvelle méthode localement multivariée basée sur une approche a contrario. La validation de cette nouvelle approche est réalisée dans deux contextes applicatifs : la détection d'anomalies de perfusion en ASL et la détection de zones d'activation en IRMf BOLD. / This thesis deals with the analysis of brain function in Magnetic Resonance Imaging (MRI) using two sequences: BOLD functional MRI (fMRI) and Arterial Spin Labelling (ASL). In this context, group statistical analyses are of great importance in order to understand the general mechanisms underlying a pathology, but there is also an increasing interest towards patient-specific analyses that draw conclusions at the patient level. Both group and patient-specific analyses are studied in this thesis. We first introduce a group analysis in BOLD fMRI for the study of specific language impairment, a pathology that was very little investigated in neuroimaging. We outline atypical patterns of functional activity and lateralisation in language regions. Then, we move forward to patient-specific analysis. We propose the use of robust estimators to compute cerebral blood flow maps in ASL. Then, we analyse the validity of the assumptions underlying standard statistical analyses in the context of ASL. Finally, we propose a new locally multivariate statistical method based on an a contrario approach and apply it to the detection of atypical patterns of perfusion in ASL and to activation detection in BOLD functional MRI.

This thesis deals with the analysis of brain function in Magnetic Resonance Imaging (MRI) using two sequences: BOLD functional MRI (fMRI) and Arterial Spin Labelling (ASL). In this context, group statistical analyses are of great importance in order to understand the general mechanisms underlying a pathology, but there is also an increasing interest towards patient-specific analyses that draw conclusions at the patient level. Both group and patient-specific analyses are studied in this thesis. We first introduce a group analysis in BOLD fMRI for the study of specific language impairment, a pathology that was very little investigated in neuroimaging. We outline atypical patterns of functional activity and lateralisation in language regions. Then, we move forward to patient-specific analysis. We propose the use of robust estimators to compute cerebral blood flow maps in ASL. Then, we analyse the validity of the assumptions underlying standard statistical analyses in the context of ASL. Finally, we propose a new locally multivariate statistical method based on an a contrario approach and apply it to the detection of atypical patterns of perfusion in ASL and to activation detection in BOLD functional MRI.