gdimap-package: Generalized Diffusion Magnetic Resonance Imaging

Description Details Note Author(s) References


The package implements algorithms to estimate and visualize the orientation of neuronal pathways in model-free methods (q-space imaging methods). For fibre orientation estimation based on mixtures of von Mises-Fischer (vMF) distributions see gqi.odfvmflines, gqi.odfvmf, sph.odfvmflines, and sph.odfvmf. For fibre orientation estimation based on local peak detection procedures see gqi.odfpeaklines, gqi.odfpeaks, sph.odfpeaklines, and sph.odfpeaks. In these names, the prefix ‘gqi’ references functions using the standard GQI method (Yeh 2010), or the GQI2 variant (Garyfallidis 2012) for ODF reconstruction. The prefix ‘sph’ references functions using spherical harmonics approximations based on Aganj's ODF reconstruction (CSA-QBI). Visualization of RGB-maps and glyph-maps is implemented through rgbvolmap and gqi.odfvxgrid, respectively. Various types of simulations of diffusion and ODF profiles, illustrating the application of vMF mixtures for fibre orientation estimation are implemented in simulglyph.vmf, simul.simplefield, simul.fandtasia. Data sets used in the examples are documented.


For a complete list of functions type library(help=gdimap).


For reasons of limited CRAN storage space, a trimmed down data set with just 4 coronal slices was selected. Coronal slices (29:32) were extracted from the original data set. Hence, the argument bview="coronal" is used in the examples, and the range of coronal slices is (1:4). User specified complete data sets may be used without restrictions.

Commonly used acronyms:
GFA - Generalized Fractional Anisotropy
ODF - Orientation Distribution Function
GQI - Generalized q-Sampling Imaging
GQI2 - Generalized q-Sampling Imaging variant
QBI - Q-ball Imaging
CSA-QBI - Constant Solid Angle QBI MRI - Magnetic Resonance Imaging
dMRI - Diffusion Magnetic Resonance Imaging
RGB maps - Red:Green:Blue color maps
HARDI - High Angular Resolution Diffusion Imaging
vMF - von Mises-Fisher


Adelino Ferreira da Silva, Universidade Nova de Lisboa, Faculdade de Ciencias e Tecnologia, Portugal, afs at


Ferreira da Silva, A. R. Computational Representation of White Matter Fiber Orientations, International Journal of Biomedical Imaging, Vol. 2013, Article ID 232143, Hindawi Publishing Corporation

Ferreira da Silva, A. R. Facing the Challenge of Estimating Human Brain White Matter Pathways. In Proc. of the 4th International Joint Conference on Computational Intelligence (Oct. 2012), K. Madani, J. Kacprzyk, and J. Filipe, Eds., SciTePress, pp. 709-714.

Hornik, K., and Gruen, B. movMF: Mixtures of von Mises-Fisher Distributions, 2012. R package version 0.1-0.

Hankin, R. K. S. Special functions in R: introducing the gsl package. R News 6 (October 2006).

Adler, D., and Murdoch, D. rgl: 3D visualization device system (OpenGL), 2012. R package version 0.92.880.

Auguie, B. gridExtra: functions in Grid graphics, 2012. R package version 0.9.1.

Barber, C. B., Habel, K., Grasman, R., Gramacy, R. B., Stahel, A., and Sterratt, D. C. geometry: Mesh generation and surface tesselation, 2012. R package version 0.3-2.

R Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2012. ISBN 3-900051-07-0.

Whitcher, B., Schmid, V. J., and Thornton, A. Working with the DICOM and NIfTI data standards in R. Journal of Statistical Software 44, 6 (2011), 1-28.

Jenkinson, M., Beckmann, C. F., Behrens, T. E., Woolrich, M. W., and Smith, S. M. FSL. NeuroImage 62, 2 (2012), 782-790.

Tuch D. S., Q-Ball Imaging, Magnetic Resonance in Medicine 52 (2004), 1358-1372.

Tabelow K., Polzehl J.: dti: DTI/DWI Analysis, 2012. R package version 1.1-0.

Polzehl J., Tabelow K., dti: Beyond the Gaussian Model in Diffusion-Weighted Imaging. Journal of Statistical Software 44, 12 (2011).

Yeh, F.-C., Wedeen, V. J., and Tseng, W.-Y. I. Generalized q-Sampling Imaging. IEEE Transactions on Medical Imaging 29, 9 (2010), 1626-1635.

Garyfallidis E., Towards an Accurate Brain Tractography, 2012, PhD Thesis, University of Cambridge.

Aganj I., Lenglet C., Sapiro G., Yacoub E., Ugurbill K. and Harel N. Reconstruction of the orientation distribution function in single- and multiple-shell q-ball imaging within constant solid angle, Magnetic Resonance in Medicine, 64(2) (2010), 554-566.

gdimap documentation built on May 29, 2017, 11:03 p.m.