GPU Accelerated Browser for Neuroimaging Genomics

Neuroimaging genomics is an emerging field that provides exciting opportunities to understand the genetic basis of brain structure and function. The unprecedented scale and complexity of the imaging and genomics data, however, have presented critical computational bottlenecks. In this work we present our initial efforts towards building an interactive visual exploratory system for mining big data in neuroimaging genomics. A GPU accelerated browsing tool for neuroimaging genomics is created that implements the ANOVA algorithm for single nucleotide polymorphism (SNP) based analysis and the VEGAS algorithm for gene-based analysis, and executes them at interactive rates. The ANOVA algorithm is 110 times faster than the 4-core OpenMP version, while the VEGAS algorithm is 375 times faster than its 4-core OpenMP counter part. This approach lays a solid foundation for researchers to address the challenges of mining large-scale imaging genomics datasets via interactive visual exploration

Robust frequency-dependent diffusion kurtosis computation using an efficient direction scheme, axisymmetric modelling, and spatial regularization

Frequency-dependent diffusion MRI (dMRI) using oscillating gradient encoding and diffusion kurtosis imaging (DKI) techniques have been shown to provide additional insight into tissue microstructure compared to conventional dMRI. However, a technical challenge when combining these techniques is that the generation of the large b-values required for DKI is difficult when using oscillating gradient diffusion encoding. While efficient encoding schemes can enable larger b-values by maximizing multiple gradient channels simultaneously, they do not have sufficient directions to enable fitting of the full kurtosis tensor. Accordingly, we investigate a DKI fitting algorithm that combines axisymmetric DKI fitting, a prior that enforces the same axis of symmetry for all oscillating gradient frequencies, and spatial regularization, which together enable robust DKI fitting for a 10-direction scheme that offers double the b-value compared to traditional direction schemes. Using data from mice (oscillating frequencies of 0, 60, and 120 Hz) and humans (0 Hz only), we first show that axisymmetric modelling is advantageous over full kurtosis tensor fitting in terms of preserving contrast and reducing noise in DKI maps, and improved DKI map quality when using an efficient encoding scheme with averaging as compared to a traditional scheme with more encoding directions. We also demonstrate how spatial regularization during fitting preserves spatial features better than using Gaussian filtering prior to fitting, which is an oft-reported preprocessing step for DKI, and that enforcing consistent axes of symmetries across frequencies improves fitting quality. Thus, the use of an efficient 10-direction scheme combined with the proposed DKI fitting algorithm provides robust maps of frequency-dependent directional kurtosis parameters that can be used to explore novel biomarkers for various pathologies.Comment: 41 pages, 9 figures, 2 supplementary figure