Investigating brain function and anatomy through ICA-based functional ultrasound imaging

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Abstract

Understanding the hidden organizational principles existing in the human brain was always one of the great challenges in Neuroscience. To uncover the way the brain functions, advancements in the fields of Medical Imaging and Computational Science have been of great importance. Powerful imaging tools, such as functional magnetic resonance imaging (fMRI) and positron emission tomography (PET), have already enabled scanning the whole brain volume and visualizing the brain functioning, both at rest and during task execution, to a significant degree. However, several limitations especially in spatiotemporal resolution led to the need for further advancements in the field of functional imaging. An alternative technique, that overcomes most of the previously existing problems, is functional ultrasound (fUS). fUS is capable of imaging even the microvasculature blood-flow dynamics in response to brain activation with high spatiotemporal resolution. The wealth of fUS-acquired data calls for advanced data-analytic methods to uncover new information, beyond the well-applied simple univariant correlation method. This is the main goal of this MSc thesis, to use a proper analysis technique, mainly borrowed from the same-principle fMRI technique, in order to produce powerful inferences. For this reason, a detailed literature review regarding fUS imaging and fMRI analysis methods is introduced. Then, the main analysis part is focused on the Independent Component Analysis (ICA) method, trying to segregate the brain into spatially independent components that share a similar activity response. Here, the whole processing pipeline is established, describing all the necessary preprocessing steps along with ICA parameters and approaches (single- and group-ICA) using the ICASSO software package. As a post-processing step, functional images-to-Allen brain atlas registration is also performed in order to identify the different regions represented in the ICA-derived spatial components. The effectiveness of the methods is assessed based on the collected results on different datasets, obtained from 2D visual-stimulation as well as 3D resting-state experiments conducted on mice at the Neuroscience department of the Erasmus MC. As a conclusion, ICA was able to separate different anatomical and functional sub-networks. More specifically, from the visual-stimulation experiments, brain regions such as Lateral geniculate nucleus (LGN) that play a role in the visual pathway are identified, while from the resting-state the spatial continuity of different regions is confirmed.