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.


Changes in gdimap version 0.1-9 o reverting to gdimap version 0.1-6 which used 'oro.nifti' for reading/writing NiFTI datasets. Reason: the package 'Rniftilib' has been removed from CRAN.

Changes in gdimap version 0.1-8 o using package 'Rniftilib' instead of 'oro.nifti' for reading/writing NiFTI datasets. Rniftilib's functions were found faster and requiring less RAM than oro.nifti's, for large datasets.

Changes in gdimap version 0.1-6

o In 'vmf' functions principal diffusion directions (PDD) are now sorted by 'alpha' (fitted mixture probabilities). o Support for non-default control parameters in 'movMF' calls o Changed normalization for glyph visualization to agree with theta/|theta|. o Eliminated 'snapshot' function args.

Changes in gdimap version 0.1-4

o minor corrections

Changes in gdimap version 0.1-1

o ODF reconstructions now supports two GQI methods (QBI and QBI2), and one QBI method. o New functions for fibre orientation estimation and visualization. o Simulations via 'simulglyph.vmf' now supports GQI, GQI2, and QBI. o The masked data set 'data_brain' has been removed since it is not used directly. o Allow fiber simulations with different volume fractions o Hacked geometry::surf.tri() to supress warnings o Filename 'dsi203_bmax4000.txt' substituted by 'btable.txt' o Format of file 'data.bvec' modified to 'scan' format as produced by the 'dcm2nii' tool, and compatible with the formats used in the 'DSI_Studio' and 'Dipy' toolboxes. o Documentation has been updated.

Changes in gdimap version 0.0-3

o Format of "data.bvec" file was modified to be specified as a matrix of size nx3. Functions were modified accordingly. o Minor corrections in examples.

Reference manual

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0.1-9 by Adelino Ferreira da Silva, 6 years ago

Browse source code at

Authors: Adelino Ferreira da Silva <[email protected]>

Documentation:   PDF Manual  

Task views: Medical Image Analysis

GPL (>= 2) license

Imports oro.nifti, movMF, grid, gridExtra, colorspace, geometry, gsl, abind

Depends on rgl

See at CRAN