gdimap: Generalized Diffusion Magnetic Resonance Imaging

Diffusion anisotropy has been used to characterize white matter neuronal pathways in the human brain, and infer global connectivity in the central nervous system. The package implements algorithms to estimate and visualize the orientation of neuronal pathways in model-free methods (q-space imaging methods). For estimating fibre orientations two methods have been implemented. One method implements fibre orientation detection through local maxima extraction. A second more robust method is based on directional statistical clustering of ODF voxel data. Fibre orientations in multiple fibre voxels are estimated using a mixture of von Mises-Fisher (vMF) distributions. This statistical estimation procedure is used to resolve crossing fibre configurations. Reconstruction of orientation distribution function (ODF) profiles may be performed using the standard generalized q-sampling imaging (GQI) approach, Garyfallidis' GQI (GQI2) approach, or Aganj's variant of the Q-ball imaging (CSA-QBI) approach. Procedures for the visualization of RGB-maps, line-maps and glyph-maps of real diffusion magnetic resonance imaging (dMRI) data-sets are included in the package.

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