Various definitions of spherical sampling
- designer.tractography.sphericalsampling.dsigrid(odf_key='odf8')¶
Reads DSIStudio’s ODF geometry in odfs.mat to use in creation of DSIStudio’s .fib file.
- Parameters
odf_keys (str; optional; {‘odf4’, ‘odf5’, ‘odf6’, ‘odf8’, ‘odf12’, ‘odf20’}) – DSIStudio’s direction set to load. (Default: ‘odf8’)
- Returns
odf_vertices (array_like(dtype=flaot64)) – ODF vertices
odf_faces (array_like(dtype=uint16)) – ODF faces
- designer.tractography.sphericalsampling.odfgrid(res='med')¶
Defines the spherical grid defined by quadrisection of the isocahedron. There are three possible options: ‘low’, ‘med’, or ‘high’, where higher resolutions cost more computational time. Use for computation of spherical harmonics from ODFs.
NOTE: These sampling directions were ported from DKE (original author: Russell Glenn)
- Parameters
res (str; optional; {‘low’, ‘med’, ‘high’}) – Resolution of spherical sampling distribution (Default: ‘med’) ‘low’ defines the spherical grid defined by 3 fold quadrisection of the isocahedron, or 8 fold tesselation of icosahedron. ‘med’ defines the spherical grid defined by 4 fold quadrisection of the isocahedron, or 16 fold tesselation of icosahedron. ‘high’ defines the spherical grid defined by 5 fold quadrisection of the isocahedron, or 24 fold tesselation of icosahedron.
- Returns
S (array_like(dtype=float64)) – Coordinates for spherical grid in polar coordinates, extends slightly over one half of the sphere to estimate local maxima on border. First column is phi, second column is theta.
idx (aarray_like(dtype=uint16)) – First column defines points in S over one half of the sphere for candiate local maxima. Columns 2-7 define the neighbors for the corresponding point in column 1.
idx8 (array_like(dtype=uint16)) – Defines vertices to undersample for sphericalgrid3 - this is useful, for example, when trying to save a smaler datastructure to load into DSI studio (all coordinates are savesd in one large file)
area (array_like(dtype=float64)) – Defines the area that each vertex encompasses. It is generally impossible to spread points out isotropically over a sphere, so the area is slightly different for each point - this can be used to update computations that occur over the spherical grid, eg GFA.
faces (array_like(dtype=uint16)) – Data structure matching S to save and load into DSI Studio for visualization
separation_angle (float64) – Average separation angle between each peak and its nearest neighbors.