Assessment of Functional Connectivity Impairment in Rat Brains

Sammanfattning: While the rodent model has long been used in brain research, there exists no standardisedprocessing routine that can be employed for analysis and investigation of disease models. Thepresent thesis attempts to investigate a diseased brain model by implementing a collection ofscripts, combined with algorithms from existing neuroimaging software, and adapting themto the rodent brain, in an attempt to examine when and how monaural canal atresia affectsthe functional connectivity of the brain. We show that it is possible to use software tailoredto the human brain to pre-process the rodent model. Following conventional pipelines andresting state functional MRI (rs-fMRI)-specific strategies, the developed processing routineimplements the most basic steps suggested in literature. On the single-subject level, skullstripping was done using Mialite software, motion correction and distortion correction werebased on FMRIB software library (FSL) algorithms and motion artefacts were removed usingICA-based Automatic Removal Of Motion Artifacts (ICA-AROMA). Following denoising,normalisation to standard space, smoothing and temporal filtering, group level analysis wasperformed. A univariate, hypothesis-driven method and a multivariate, data-driven methodwere used for group comparison and statistical inference. While seed-based correlationanalysis (SCA) did not return any significant results, independent component analysis (ICA) identified two components that show activation in areas of interest.