simul.fandtasia
(Package: gdimap) :
Simulation of Curved Fibre Bundles for von Mises-Fisher Fibre Orientation Mapping
The synthesized field of diffusion profiles generated by simul.fandtasia are used to reconstruct ODF profiles using the GQI method. ODF profiles and fibre directions are estimated by relying on von Mises-Fisher (vMF) distributions for directional mapping.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: simul.fandtasia
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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 et.al. 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.
● Data Source:
CranContrib
● Keywords: package
● Alias: gdimap-package
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sph.odfpeaklines
(Package: gdimap) :
Fibre Orientation Mapping Based on Local Peak Detection with QBI Reconstruction
sph.odfpeaklines produces line-maps of ODF profiles for diffusion data slices using a regularized spheric harmonics method for ODF reconstruction.
● Data Source:
CranContrib
● Keywords: dplot, methods, utilities
● Alias: sph.odfpeaklines
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sph.odfvmflines
(Package: gdimap) :
Fibre Orientation Mapping Based on von Mises-Fisher Distributions with QBI reconstruction
In order to enable mapping complex white matter fibres in the brain, sph.odfvmflines implements a new methodology based on directional statistics to estimate fibre profiles from high angular resolution diffusion imaging data. Statistical orientation estimation in sph.odfvmf is based on von Mises-Fisher clustering procedures provided by the R-package movMF, by Kurt Hornik and Bettina Gruen.
● Data Source:
CranContrib
● Keywords: clustering, dplot, methods
● Alias: sph.odfvmflines
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sph.odfvmf
(Package: gdimap) :
Fibre Orientation Estimation Based on von Mises Distributions with Q-ball Reconstruction
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 mappings.
● Data Source:
CranContrib
● Keywords: clustering, methods
● Alias: sph.odfvmf
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dec
(Package: gdimap) :
Directionally-Encoded Color (DEC) Representation
dec illustrates the RGB encoding used in DEC representations
● Data Source:
CranContrib
● Keywords: dplot
● Alias: dec
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data_brain_mask
(Package: gdimap) :
Example of Mask File Used in Diffusion MRI Processing
The ‘data_brain_mask.nii.gz’ dataset defines the mask used in the diffusion MRI analysis for ‘data.nii.gz’.
● Data Source:
CranContrib
● Keywords: data
● Alias: data_brain_mask
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niinorm
(Package: gdimap) :
Normalization of Principal Diffusion Directions
niinorm normalizes Principal Diffusion Directions (PDDs) in NIfTI files. The unnormalized PDD values produced by gqi.odfvmf retain information about the estimated von Mises-Fisher parameters at each voxel, which are useful in probabilistic tractography. On the other hand, normalized PDD values are useful for visualization and seed mask creation, namely using the ‘FSL/fslview’ tool.
● Data Source:
CranContrib
● Keywords: utilities
● Alias: niinorm
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slfcst
(Package: gdimap) :
A Region-of-Interest (ROI) File for Diffusion MRI Analysis
The ‘slfcst.nii.gz’ is a region-of-interest (ROI) file that was formed by extracting the superior longitudinal fasciculus (SLF) and corticospinal tract (CST) regions from the main data diffusion set ‘data.nii.gz’.
● Data Source:
CranContrib
● Keywords: data
● Alias: slfcst
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gqi.odfpeaklines
(Package: gdimap) :
Fibre Orientation Mapping Based on Local Peak Detection
gqi.odfpeaklines produces line-maps of ODF profiles for diffusion data slices.
● Data Source:
CranContrib
● Keywords: dplot, methods, utilities
● Alias: gqi.odfpeaklines
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