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dipy.reconst.gqi

Classes and functions for generalized q-sampling

class dipy.reconst.gqi.GeneralizedQSampling(data, bvals, gradients, Lambda=1.2, odf_sphere='symmetric362', mask=None)

Implements Generalized Q-Sampling

Generates a model-free description for every voxel that can be used from simple to very complicated configurations like quintuple crossings if your datasets support them.

You can use this class for every kind of DWI image but it will perform much better when you have a balanced sampling scheme.

Implements equation [9] from Generalized Q-Sampling as described in Fang-Cheng Yeh, Van J. Wedeen, Wen-Yih Isaac Tseng. Generalized Q-Sampling Imaging. IEEE TMI, 2010.

Parameters :

data : array,

shape(X,Y,Z,D)

bvals : array,

shape (N,)

gradients : array,

shape (N,3) also known as bvecs

Lambda : float,

smoothing parameter - diffusion sampling length

Notes

In order to reconstruct the spin distribution function a nice symmetric evenly distributed sphere is provided using 362 or 642 points. This is usually sufficient for most of the datasets.

Methods

ind() indices on the sampling sphere
npa(s[, width]) non-parametric anisotropy
odf(s) spin density orientation distribution function
qa() quantitative anisotropy
ind()

indices on the sampling sphere

npa(s, width=5)

non-parametric anisotropy

Nimmo-Smith et. al ISMRM 2011

odf(s)

spin density orientation distribution function

Parameters :

s : array, shape(D),

diffusion signal for one point in the dataset

Returns :

odf : array, shape(len(odf_vertices)),

spin density orientation distribution function

qa()

quantitative anisotropy

dipy.reconst.gqi.equatorial_zone_vertices(vertices, pole, width=5)

finds the ‘vertices’ in the equatorial zone conjugate to ‘pole’ with width half ‘width’ degrees

dipy.reconst.gqi.patch_vertices(vertices, pole, width)

find ‘vertices’ within the cone of ‘width’ degrees around ‘pole’

dipy.reconst.gqi.polar_zone_vertices(vertices, pole, width=5)

finds the ‘vertices’ in the equatorial band around the ‘pole’ of radius ‘width’ degrees

dipy.reconst.gqi.upper_hemi_map(v)

maps a 3-vector into the z-upper hemisphere