mcot.gcoord.radial_transition

Script that fits a sigmoid to the radial index across the white/gray matter boundary.

Functions

model(radial_index, white[, affine, …])

Creates a probabilistic model of the transition across the white/gray matter bounary.

run_from_args(args)

model

mcot.gcoord.radial_transition.model(radial_index, white, affine=None, surf_mask=None, min_dist=- 2.0, smooth_weight=0.7, watson=False, idx_vertex=None, dist=None)[source]

Creates a probabilistic model of the transition across the white/gray matter bounary.

Parameters

  • radial_index – (Nx, Ny, Nz) array with the radial index

  • white – white/gray matter boundary

  • affine – (4, 4) array with the transformation from voxel to mm space

  • surf_mask – (Nvertex, ) boolean array, which is True on vertices to be included in the fit

  • min_dist – only include voxels within this distance from WM/GM boundary

  • smooth_weight – weighting for the smoothing parameter

  • watson – assume a Watson distribution for the radial index rather than a normal distribution

  • idx_vertex – (Nx, Ny, Nz) array with index of closest vertex

  • dist – distance from the WM/GM boundary

Returns

pymc3 model which fits the sigmoidal transition across the surface

run_from_args

mcot.gcoord.radial_transition.run_from_args(args)[source]