Comparative mouse brain tractography of diffusion magnetic resonance imaging

Abstract

Diffusion magnetic resonance imaging (dMRI) tractography can be employed to simultaneously analyse three-dimensional white matter tracts in the brain. Numerous methods have been proposed to model diffusion-weighted magnetic resonance data for tractography, and we have explored the functionality of some of these for studying white and grey matter pathways in ex vivo mouse brain. Using various deterministic and probabilistic algorithms across a range of regions of interest we found that probabilistic tractography provides a more robust means of visualizing both white and grey matter pathways than deterministic tractography. Importantly, we demonstrate the sensitivity of probabilistic tractography profiles to streamline number, step size, curvature, fiber orientation distribution, and whole-brain versus region of interest seeding. Using anatomically well-defined cortico-thalamic pathways, we show how density maps can permit the topographical assessment of probabilistic tractography. Finally, we show how different tractography approaches can impact on dMRI assessment of tract changes in a mouse deficient for the frontal cortex morphogen, fibroblast growth factor 17. In conclusion, probabilistic tractography can elucidate the phenotypes of mice with neurodegenerative or neurodevelopmental disorders in a quantitative manner.

Mapping somatosensory connectivity in adult mice using diffusion MRI tractography and super-resolution track density imaging

“…DWI data were acquired in accordance with protocols previously described (Calamante et al, 2012b;Moldrich et al, 2010). In brief, data were acquired on a 16.4 Tesla vertical bore animal system (Bruker Biospin, Germany) using a Micro2.5 gradient system and a 15 mm linear surface coil (M2M, Australia).…”

“…Diffusion MRI is an important mapping tool for tissue structure and connectivity, including information about fibre orientation and integrity and has been used to visualize tissue microstructure in humans and animal models (Behrens et al, 2003;Calamante et al, 2012a;Calamante et al, 2010;Jiang and Johnson, 2011;Kim et al, 2012;Moldrich et al, 2010).…”

Diffusion-weighted magnetic resonance imaging detection of basal forebrain cholinergic degeneration in a mouse model

“…After perfusion, mouse brains were washed in PBS for 4 days, after which they were immersed in Fomblin oil (Y06/6 grade, Solvay, NY) and diffusion weighted magnetic resonance images were acquired according to the protocol of Moldrich et al (2010). Briefly, we used a small animal MRI system (16.4 T vertical bore; Bruker Biospin, Rheinstetten, Germany; ParaVision v5.0) with a 15 mm linear SAW coil (M2MImaging, Brisbane, Australia).…”

“…Probabilistic tractography was performed with MRtrix, creating whole brain tractograms by seeding every voxel five times and using tracking parameters optimized for mouse brain (step size = 0.01 mm, curvature = 0.07 mm, seeds/voxel = 5; (Moldrich et al, 2010). …”

An ontologically consistent MRI-based atlas of the mouse diencephalon

“…However, segmentation of T 2 *-weighted MR images of the diencephalon is challenging; in comparison to the hippocampus, which has clear boundaries between layers, and the cerebellum, which has clear structural boundaries, many parts of the diencephalon possess relatively subtle variations in contrast. In many previous MR studies in the components of the thalamus were not identified (Dorr et al, 2008), with the study by Moldrich et al (2010) being the only one to attempt to segment the thalamus.…”