cortex.polyutils.FlatSlab

class cortex.polyutils.FlatSlab(flat, wm, pia, polys, correlation_length=0.5, polish=3.0, detrend=64.0)

The cortical slab’s relief, as an offset from the flat white surface.

folding_height, smoothed and with the whole-map swell taken out.

Parameters:

flat2D ndarray, shape (total_verts, 3)

Location of each vertex in flatmap space. Only the first two columns are used; the flatmap is taken to lie in the z = 0 plane.

wm, pia2D ndarray, shape (total_verts, 3)

The white matter and pial surfaces.

polys2D ndarray, shape (total_polys, 3)

Triangle vertex indices of the flat surface. Vertices in no triangle – the medial wall, which is cut away from the flatmap – get a zero offset.

correlation_lengthfloat, optional

Length scale over which the height ratio is regularised – enough to stop a vertex whose white matter area nearly vanishes from spiking.

polishfloat, optional

Smoothing of the finished relief, as a diffusion time. Beware the scale: t halves a wavelength of 2 * pi * sqrt(t), so the default cuts at 11 mm and not, as it looks, at 3. Much more takes the gyri too.

detrendfloat, optional

Wavelength above which the relief is flattened. Cortex is regionally thicker in some lobes than others, and on S1 that swell is a third of the relief’s variance in one map-spanning mode – real, but not folding, and the viewer’s scale setting multiplies it along with everything else. Pass 0 to keep it.

Attributes:

infodict

Height statistics from the last computed relief.

Methods

__init__(flat, wm, pia, polys[, ...])

Attributes

relaxed

The pial surface's height above the flat white matter surface.