Schizophrenia is a complex and severe psychiatric disorder with positive symptoms, negative symptoms and cognitive deficits. Preclinical neurobiological studies showed that alterations of dopaminergic and glutamatergic neurotransmitter circuits involving the prefrontal cortex resulted in cognitive impairment such as working memory. Functional activation and functional connectivity findings of functional Magnetic Resonance Imaging (fMRI) data provided support for prefrontal dysfunction during fMRI working memory tasks in individuals with schizophrenia. However, these findings do not offer a neurobiological interpretation of the fMRI data. Biophysical modelling of functional large-scale networks has been designed for the analysis of fMRI data, which can be interpreted in a mechanistic way. This approach may enable the interpretation of fMRI data in terms of altered synaptic plasticity processes found in schizophrenia. One such process is gating mechanism, which has been shown to be altered for the thalamo-cortical and meso-cortical connection in schizophrenia. The primary aim of the thesis was to investigate altered synaptic plasticity and gating mechanisms with Dynamic Causal Modelling (DCM) within functional large-scale networks during two fMRI tasks in individuals with schizophrenia. Applying nonlinear DCM to the verbal fluency fMRI task of the Edinburgh High Risk Study, we showed that the connection strengths with nonlinear modulation for the thalamo-cortical connection was reduced in subjects at high familial risk of schizophrenia when compared to healthy controls. These results suggest that nonlinear DCM enables the investigation of altered synaptic plasticity and gating mechanism from fMRI data. For the Scottish Family Mental Health Study, we reported two different optimal linear models for individuals with established schizophrenia (EST) and healthy controls during working memory function. We suggested that this result may indicate that EST and healthy controls used different functional large-scale networks. The results of nonlinear DCM analyses may suggest that gating mechanism was intact in EST and healthy controls. In conclusion, the results presented in this thesis give evidence for the role of synaptic plasticity processes as assessed in functional large-scale networks during cognitive tasks in individuals with schizophrenia.

Modelling neuronal interactions using a directed network can be used to provide insight into the activity of the brain during experimental tasks. Magnetoencephalography (MEG) allows for the observation of the fast neuronal dynamics necessary to characterize the activity of sources and their interactions. A network representation of these sources and their connections can be formed by mapping them to nodes and their connection strengths to edge weights. Dynamic Causal Modelling (DCM) presents a Bayesian framework to estimate the parameters of these networks, as well as the ability to test hypotheses on the structure of the network itself using Bayesian model comparison. DCM uses a neurologically-informed representation of the active neural sources, which leads to an underdetermined system and increased complexity in estimating the network parameters. This work shows that inform- ing the MEG DCM source location with prior distributions defined using a MEG source localization algorithm improves model selection accuracy. DCM inversion of a group of candidate models shows an enhanced ability to identify a ground-truth network structure when source-localized prior means are used. / Master of Science

Master’s thesis is aimed at familiarization with the principles of measurement and data processing functional magnetic resonance, focusing on the analysis of effective connectivity using dynamic causal modelling (DCM). The practical part includes three main thematic areas relating to the description of the processing and evaluation of measured or simulated data. First, there is on sample dataset described the neuroscientific SPM toolbox to analyze measured data. Then follows introduction of the proposed approach with which is investigated the behavior of the model estimation neural interactions with respect to the change of input parameters. This phenomenon is also simulated and on base of achieved results is recommended optimal approach to analyzing effective connectivity using dynamic causal modeling for the group of subjects. The last circuit in the practical part is assessment of shift the coordinates of brain areas on dynamic causal modelling results for the group of subjects from the data obtained from real measurements. Obtained results from simulated data and the results obtained from measured data are evaluated and discussed in the final part.

The blood oxygen level dependent functional MRI (BOLD-fMRI) signal is an indirect measure of the neuronal activity that most BOLD studies are interested in. This thesis uses generative embedding algorithms to investigate some of the challenges and opportunities that this presents for BOLD imaging. It is standard practice to analyse BOLD signals using general linear models (GLMs) that assume fixed neurovascular coupling. However, this assumption may cause false positive or negative neural activations to be detected if the biological manifestations of brain diseases, disorders and pharmaceutical drugs (termed "neuromodulations") alter this coupling. Generative embedding can help overcome this problem by identifying when a neuromodulation confounds the standard GLM. When applied to anaesthetic neuromodulations found in preclinical imaging data, Fentanyl has the smallest confounding effect and Pentobarbital has the largest, causing extremely significant neural activations to go undetected. Half of the anaesthetics tested caused overestimation of the neuronal activity but the other half caused underestimation. The variability in biological action between anaesthetic modulations in identical brain regions of genetically similar animals highlights the complexity required to comprehensively account for factors confounding neurovascular coupling in GLMs generally. Generative embedding has the potential to augment established algorithms used to compensate for these variations in GLMs without complicating the standard (ANOVA) way of reporting BOLD results. Neuromodulation of neurovascular coupling can also present opportunities, such as improved diagnosis, monitoring and understanding of brain diseases accompanied by neurovascular uncoupling. Information theory is used to show that the discriminabilities of neurodegenerative-diseased and healthy generative posterior parameter spaces make generative embedding a viable tool for these commercial applications, boasting sensitivity to neurovascular coupling nonlinearities and biological interpretability. The value of hybrid neuroimaging systems over separate neuroimaging technologies is found to be greatest for early-stage neurodegenerative disease.

This PhD thesis investigated the role of the basal ganglia in memory and motor inhibition. Recent neuroimaging evidence suggests a supramodal network of inhibition involving the lateral prefrontal cortex. Here we examined whether this supramodal network also includes subcortical structures, such as the basal ganglia. Despite their well-established role in motor control, the basal ganglia are repeatedly activated but never interpreted during memory inhibition. We first used a series of meta-analyses to confirm the consistent involvement of the basal ganglia across studies using memory and motor inhibition tasks (including the Go/No-Go, Think/No-Think, and Stop-signal tasks), and discovered that there may be different subprocesses of inhibition. For instance, while the Go/No-Go task may require preventing a response from taking place, the Think/No-Think and Stop-signal tasks may require cancelling an emerging or ongoing response. We then conducted an fMRI study to examine how the basal ganglia interact with other putative supramodal regions (e.g., DLPFC) to achieve memory and motor inhibition during prevention and cancellation. Through dynamic causal modelling (DCM), we found that both DLPFC and basal ganglia play effective roles to achieve inhibition in the task-specific regions (hippocampus for memory inhibition; primary motor cortex (M1) for motor inhibition). Specifically, memory inhibition requires a DLPFC-basal ganglia-hippocampus pathway, whereas motor inhibition requires a basal ganglia-DLPFC-M1 pathway. We correlated DCM coupling parameters with behavioural indices to examine the relationship between network dynamics during prevention and cancellation and the successfulness of inhibition. However, due to constraints with DCM parameter estimates, caution is necessary when interpreting these results. Finally, we used diffusion weighted imaging to explore the anatomical connections supporting functions and behaviour. Unfortunately, we were unable to detect any white matter variability in relation to effective connectivity or behaviour during the prevention or cancellation processes of memory and motor inhibition at this stage. This PhD thesis provides essential INITIAL evidence that not only are the basal ganglia consistently involved in memory and motor inhibition, but these structures are effectively engaged in these tasks, achieving inhibition through task-specific pathways. We will discuss our findings, interpretations, and future directions in the relevant chapters.

This thesis deals with functional magnetic resonance imaging (fMRI), in particular with dynamic causal modelling (DCM) as one of the methods for effective brain connectivity analysis. It has been studied the effect of signal coordinates selection, which was used as an input of DCM analysis, on its results based on simulated data testing. For this purpose, a data simulator has been created and described in this thesis. Furthermore, the methodology of testing the influence of the coordinates selection on DCM results has been reported. The coordinates shift rate has been simulated by adding appropriate levels of various types of noise signals to the BOLD signal. Consequently, the data has been analyzed by DCM. The program has been supplemented by a graphical user interface. To determine behaviour of the model, Monte Carlo simulations have been applied. Results in the form of dependence of incorrectly estimated connections between brain areas on the level of the noise signals have been processed and discussed.