Local structure and global connectivity in the cerebral cortex: neuroinformatics, histology and ultra high resolution diffusion MRI in the rhesus and marmoset monkey brain

This thesis concerns the cortical connectivity in Primates. The efficacy of Diffusion weighted MRI (dMRI) is examined. White matter (“WM”) systems subjacent to cortex (“superficial WM” ) are found to be a limiting factor to dMRI tractography. Superficial WM systems are examined with dMRI itself, and with analysis of histological data from the scanned brains. dMRI data was acquired ex-vivo at exceptional spatial and angular resolution (250µm in Rhesus, 150µm in Marmoset). The superficial WM was found to be complex, and with current dMRI methods, an effective barrier to tracking to and from around 50% of cortex in Rhesus. The quality of our data allowed Gray matter seeding, so that penetration both into and out of cortex was examined. We summarize the history of cortical connectivity and current work in tractography. We present an account of the formation and properties of the superficial WM. We compare tracking behaviors to tracer results, and develop a series of scalar maps on cortical surface models to summarize tracking behaviors. We attempt to explain these maps by examining the underlying tracking behavior and the brain tissue itself, revealing the intricate nature of the superficial WM. Chapter 4 contains a separate but related project in which a histologically accurate high resolution 3D and surface atlas of the Rhesus cortex is constructed with unprecedented accuracy. A method to rapidly and accurately non-linearly transform the atlas to a scan of another animal is developed, thus labelling its cortex. accuracy is by comparison to histology of the scanned animals.