New MRI, 18F-DOPA and 11C-(+)-alpha-dihydrotetrabenazine templates for Macaca fascicularis neuroimaging: advantages to improve PET quantification

Normalization of neuroimaging studies to a stereotaxic space allows the utilization of standard volumes of interest (VOIs) and voxel-based analysis (SPM). Such spatial normalization of PET and MRI studies requires a high quality template image. The aim of this study was to create new MRI and PET templates of 18F-DOPA and 11C-(+)-α-dihydrotetrabenazine (11C-DTBZ) of the Macaca fascicularis brain, an important animal model of Parkinson's disease. MRI template was constructed as a smoothed average of the scans of 15 healthy animals, previously transformed into the space of one representative MRI. In order to create the PET templates, 18F-DOPA and 11C-DTBZ PET of the same subjects were acquired in a dedicated small animal PET scanner and transformed to the created MRI template space. To validate these templates for PET quantification, parametric values obtained with a standard VOI-map applied after spatial normalization to each template were statistically compared to results computed using individual VOIs drawn for each animal. The high correlation between both procedures validated the utilization of all the templates, improving the reproducibility of PET analysis. To prove the utility of the templates for voxel-based quantification, dopamine striatal depletion in a representative monkey treated with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was assessed by SPM analysis of 11C-DTBZ PET. A symmetric reduction in striatal 11C-DTBZ uptake was detected in accordance with the induced lesion. In conclusion, templates of M. fascicularis brain have been constructed and validated for reproducible and automated PET quantification. All templates are electronically available via the internet

Common Atlas Format and 3D Brain Atlas Reconstructor: Infrastructure for Constructing 3D Brain Atlases

One of the challenges of modern neuroscience is integrating voluminous data of diferent modalities derived from a variety of specimens. This task requires a common spatial framework that can be provided by brain atlases. The first atlases were limited to two-dimentional presentation of structural data. Recently, attempts at creating 3D atlases have been made to offer navigation within non-standard anatomical planes and improve capability of localization of different types of data within the brain volume. The 3D atlases available so far have been created using frameworks which make it difficult for other researchers to replicate the results. To facilitate reproducible research and data sharing in the field we propose an SVG-based Common Atlas Format (CAF) to store 2D atlas delineations or other compatible data and 3D Brain Atlas Reconstructor (3dBAR), software dedicated to automated reconstruction of three-dimensional brain structures from 2D atlas data. The basic functionality is provided by (1) a set of parsers which translate various atlases from a number of formats into the CAF, and (2) a module generating 3D models from CAF datasets. The whole reconstruction process is reproducible and can easily be configured, tracked and reviewed, which facilitates fixing errors. Manual corrections can be made when automatic reconstruction is not sufficient. The software was designed to simplify interoperability with other neuroinformatics tools by using open file formats. The content can easily be exchanged at any stage of data processing. The framework allows for the addition of new public or proprietary content

Brain connectivity studied by fMRI: homologous network organization in the rat, monkey, and human

The mammalian brain is composed of functional networks operating at different spatial and temporal scales — characterized by patterns of interconnections linking sensory, motor, and cognitive systems. Assessment of brain connectivity has revealed that the structure and dynamics of large-scale network organization are altered in multiple disease states suggesting their use as diagnostic or prognostic indicators. Further investigation into the underlying mechanisms, organization, and alteration of large-scale brain networks requires homologous animal models that would allow neurophysiological recordings and experimental manipulations. My current dissertation presents a comprehensive assessment and comparison of rat, macaque, and human brain networks based on evaluation of intrinsic low-frequency fluctuations of the blood oxygen-level-dependent (BOLD) fMRI signal. The signal fluctuations, recorded in the absence of any task paradigm, have been shown to reflect anatomical connectivity and are presumed to be a hemodynamic manifestation of slow fluctuations in neuronal activity. Importantly, the technique circumvents many practical limitations of other methodologies and can be compared directly between multiple species. Networks of all species were found underlying multiple levels of sensory, motor, and cognitive processing. Remarkable homologous functional connectivity was found across all species, however network complexity was dramatically increased in primate compared to rodent species. Spontaneous temporal dynamics of the resting-state networks were also preserved across species. The results demonstrate that rats and macaques share remarkable homologous network organization with humans, thereby providing strong support for their use as an animal model in the study of normal and abnormal brain connectivity as well as aiding the interpretation of electrophysiological recordings within the context of large-scale brain networks

Functional and structural connectivity in the motor system in healthy people and in patients with Parkinson’s disease

Parkinson’s disease is the second most frequent chronic neurodegenerative disorder affecting up to 2% of individuals aged 65 years and older. This pathology affects the motor processes determining the patients to have significant difficulties in daily chores. We analysed the influence of transcranial magnetic stimulation on the reaction time in 14 patients with Parkinson’s disease and 13 healthy controls. In a second study we measured the cortical thickness, cortical area and the volumes of thalamus, caudate nucleus, putamen and pallidum of 84 patients and 43 healthy controls. Our results revealed a slower reaction time in patients with Parkinson’s disease when compared to healthy controls. The reaction time was quicker in both groups after applying the magnetic stimulation pulse but patients with Parkinson’s disease still had a slower reaction time compared to healthy controls. Reaction time parameters correlated with a higher cortical thickness in the cingulate motor region and with a lower cortical thickness in the temporal and parietal regions. The second study showed decreased cortical thickness and surface area in Parkinson’s disease patients in the primary motor area, ventral premotor area and the supplementary motor cortex. Decreased cortical area in the motor regions correlated positively with the volumes of the caudate nucleus, putamen and pallidum. The present study shows a different pattern of functional and structural interactions in the motor regions in patients with Parkinson’s disease. Specifically functional and structural connectivity changes due to impaired reaction time were detected in the cingulate motor area, ventral premotor and supplementary motor areas Furthermore, cortical remodelling in PD are associated with changes in the volumes of the caudate nucleus, putamen and pallidum. Both degeneration processes as well as compensatory mechanisms of the brain can explain these changes

Experimental and Model-based Approaches to Directional Thalamic Deep Brain Stimulation

University of Minnesota Ph.D. dissertation. September 2016. Major: Biomedical Engineering. Advisor: Matthew Johnson. 1 computer file (PDF); xii, 181 pages.Deep brain stimulation (DBS) is an effective surgical procedure for the treatment of several brain disorders. However, the clinical successes of DBS hinges on several factors. Here, we describe the development of tools and methodologies in the context of thalamic DBS for essential tremor (ET) to address three key challenges: 1) accurate localization of nuclei and fiber pathways for stimulation, 2) model-based programming of high-density DBS electrode arrays (DBSA) and 3) in vivo assessment of computational DBS model predictions. We approached the first challenge through a multimodal imaging approach, utilizing high-field (7T) susceptibility-weighted imaging and diffusion-weighted imaging data. A nonlinear image deformation algorithm was used in conjunction with probabilistic fiber tractography to segment individual thalamic sub-nuclei and reconstruct their afferent fiber pathways. We addressed the second challenge by developing subject-specific computational model-based algorithms built on maximizing population activating function values within a target region using convex optimization principles. The algorithms converged within seconds and only required as many finite-element simulations as the number of electrodes on the DBSA being modeled. For the third challenge, we recorded (in two non-human primates) unit-spike data from neurons in the vicinity of chronically implanted thalamic DBSAs before, during and after high-frequency stimulation. A novel entropy-based method was developed to quantify the degree and significance of stimulation-induced changes in neuronal firing pattern. Results indicated that neurons modulated by thalamic DBS were distributed and not confined to the immediate proximity of the active electrode. For those that were modulated by DBS, their responses increasingly shifted from firing rate modulation to firing pattern modulation with increased stimulation amplitude. Additionally, strong low-pass filtering effect was observed where <4% of DBS pulses produced phase-locked spikes in cells exhibiting significant excitatory firing pattern modulation. Finally, we quantified the spatial distribution of neurons modulated by DBS by developing a novel spherical statistical framework for analysis. Together, these tools and methodologies are poised to improve our understanding of DBS mechanisms and improve the efficacy and efficiency of DBS therapy

A primate model of human cortical analysis of auditory objects

PhD ThesisThe anatomical organization of the auditory cortex in old world monkeys is similar to that in humans. But how good are monkeys as a model of human cortical analysis of auditory objects? To address this question I explore two aspects of auditory objectprocessing: segregation and timbre. Auditory segregation concerns the ability of animals to extract an auditory object of relevance from a background of competing sounds. Timbre is an aspect of object identity distinct from pitch. In this work, I study these phenomena in rhesus macaques using behaviour and functional magnetic resonance imaging (fMRI). I specifically manipulate one dimension of timbre, spectral flux: the rate of change of spectral energy.I present this thesis in five chapters. Chapter 1 presents background on auditory processing, macaque auditory cortex, models of auditory segregation, and dimensions of timbre. Chapter 2 presents an introduction to fMRI, the design of the fMRI experiments and analysis of fMRI data, and macaque behavioural training techniques employed. Chapter 3 presents results from the fMRI and behavioural experiments on macaques using a stochastic figure-ground stimulus. Chapter 4 presents the results from the fMRI experiment in macaques using spectral flux stimulus. Chapter 5 concludes with a general discussion of the results from both the studies and some future directions for research.In summary, I show that there is a functional homology between macaques and humans in the cortical processing of auditory figure-ground segregation. However, there is no clear functional homology in the processing of spectral flux between these species. So I conclude that, despite clear similarities in the organization of the auditory cortex and processing of auditory object segregation, there are important differences in how complex cues associated with auditory object identity are processed in the macaque and human auditory brains.Wellcome Trust U

Imaging the subthalamic nucleus in Parkinson’s disease

This thesis is comprised of a set of work that aims to visualize and quantify the anatomy, structural variability, and connectivity of the subthalamic nucleus (STN) with optimized neuroimaging methods. The study populations include both healthy cohorts and individuals living with Parkinson's disease (PD). PD was chosen specifically due to the involvement of the STN in the pathophysiology of the disease. Optimized neuroimaging methods were primarily obtained using ultra-high field (UHF) magnetic resonance imaging (MRI). An additional component of this thesis was to determine to what extent UHF-MRI can be used in a clinical setting, specifically for pre-operative planning of deep brain stimulation (DBS) of the STN for patients with advanced PD. The thesis collectively demonstrates that i, MRI research, and clinical applications must account for the different anatomical and structural changes that occur in the STN with both age and PD. ii, Anatomical connections involved in preparatory motor control, response inhibition, and decision-making may be compromised in PD. iii. The accuracy of visualizing and quantifying the STN strongly depends on the type of MR contrast and voxel size. iv, MRI at a field strength of 3 Tesla (T) can under certain circumstances be optimized to produce results similar to that of 7 T at the expense of increased acquisition time

Functional imaging of response selection

The functions of the prefrontal cortex remain controversial. Electrophysio- logical and lesion studies in monkeys have emphasised a role in working memory. In contrast, human functional neuroimaging studies and neuropsychology have emphasised a role in executive processes and volition. An alternative interpretation of the role of the prefrontal cortex is proposed in this thesis: that the prefrontal cortex mediates the attentional selection of sensory, mnemonic and motor representations in non-prefrontal cortex. This hypothesis is tested in a series of functional imaging experiments. In the first two experiments (chapters 4 and 5), event-related functional magnetic resonance imaging (fMRI) was used to re-examine the role of the prefrontal cortex in spatial and spatio-temporal working memory. Maintenance of information in memory was associated with activation of posterior prefrontal cortex (area 8). In contrast, the selection of an item from several remembered items was associated with activation of the middle and anterior parts of the prefrontal cortex (including area 46). To test the generalisation of 'selection' as a function of prefrontal cortex, experiment three (chapter 6) required subjects to select either a finger to move, or a colour from a multicolour display. Free selection was associated with activation of the prefrontal cortex (area 46) bilaterally, regardless of sensory or motor modality. The selection of voluntary actions has been proposed to depend on top-down modulation of motor regions by prefrontal cortex. The fourth and fifth experiments used structural equation modelling of fMRI time -series to measure the effective connectivity among prefrontal, premotor and parietal cortex. In young (chapter 7) and old (chapter 8) normal subjects, attention to action specifically enhanced coupling between prefrontal and premotor regions. This effect was not seen in patients with Parkinson's disease (chapter 8). Lastly, positron emission tomography was used to study planning in the Tower of London task, a common clinical measure of prefrontal function. Several variants of the task were developed, to distinguish the neural basis of the task's multiple cognitive components (chapter 9). The prefrontal cortex was activated in association with generation, selection or memory for moves, rather than planning towards a specified goal. The results support a generalised role in attentional selection of neuronal representations, whether stimuli, actions, or remembered items. The hypothesised attentional selection of responses is consistent with the activation of prefrontal cortex in working memory tasks and during attention to voluntary action. This role is compatible with the neurophysiological properties of individual neurons in the prefrontal cortex and the results of neuroimaging and lesion studies

Application of MRI Connectivity in Stereotactic Functional Neurosurgery

This thesis examines potential applications of advanced MRI-connectivity studies in stereotactic functional neurosurgery. Several new analysis methodologies are employed to: (1) build predictive models of DBS surgery outcome; (2) refine the surgical target and (3) help build a better understanding of the pathogenesis of the treated conditions and the mechanism of action of DBS therapy. The experimental component is divided into three main parts focusing on the following pathologies: (1) Parkinson’s disease (PD), (2) tremor and (3) trigeminal autonomic cephalalgias (TAC). Section I: In the first experiment (chapter 3), resting state fMRI was used to find radiological biomarkers predictive of response to L-DOPA in 19 patients undergoing subthalamic nucleus (STN) DBS for PD. A greater improvement in UPDRS-III scores following L-DOPA administration was characterized by higher resting state functional connectivity (fcMRI) between the prefrontal cortex and the striatum (p=0.001) and lower fcMRI between the pallidum (p=0.001), subthalamic nucleus (p=0.003) and the paracentral lobule. In the second experiment (chapter 4), structural (diffusion) connectivity was used to map out the influence of the hyperdirect pathways on outcome and identify the therapeutic ‘sweet spots’ in twenty PD patients undergoing STN-DBS. Clusters corresponding to maximum improvement in symptoms were in the posterior, superior and lateral portion of the STN. Greater connectivity to the primary motor area, supplementary motor area and prefrontal cortex was predictive of higher improvement in tremor, bradykinesia and rigidity, and rigidity respectively. The third experiment (chapter 5) examined pyramidal tract (PT) activation in 20 PD patients with STN-DBS. Volume of tissue activation (VTA) around DBS contacts were modelled in relation to the PT. VTA/ PT overlap predicted EMG activation thresholds. Sections II: Pilot data suggest that probabilistic tractography techniques can be used to segment the ventrolateral (VL) and ventroposterior (VP) thalamus based on cortical and cerebellar connectivity in nine patients who underwent thalamic DBS for tremor (chapter 6). The thalamic area, best representing the ventrointermedialis nucleus (VIM), was connected to the contralateral dentate cerebellar nucleus. Streamlines corresponding to the dentato-rubro-thalamic tract (DRT) connected M1 to the contralateral dentate nucleus via the dentato-thalamic area. Good response was seen when the active contact’s VTA was in the thalamic area with the highest connectivity to the contralateral dentate nucleus. Section III: The efficacy and safety of DBS in the ventral tegmental area (VTa) in the treatment of chronic cluster headache (CH) and short lasting unilateral neuralgiform headache attacks (SUNA) were examined (chapters 7 and 8). The optimum stimulation site within the VTa that best controls symptoms was explored (chapter 9). The average responders’ deep brain stimulation activation volume lay on the trigemino-hypothalamic tract, connecting the trigeminal system and other nociceptive brainstem nuclei, with the hypothalamus, and the prefrontal and mesial temporal areas