mvpa2.misc.surfing.volsurf.VolSurf¶

class
mvpa2.misc.surfing.volsurf.
VolSurf
(vg, white, pial, intermediate=None)¶ Associates a volume geometry with two surfaces (pial and white).
Attributes
intermediate_surface
Returns the nodewise average of the pial and white surface pial_surface
Returns the pial surface volgeom
Returns the volume geometry white_surface
Returns the white surface Methods
coordinates_to_grey_distance_mm
(nodes, xyz)Computes the grey position of coordinates in metric units surf_project_nodewise
(xyz)Projects coordinates on lines connecting pial and white matter. surf_project_weights
(nodes, xyz)Computes relative position of xyz on lines from pial to white matter. surf_project_weights_nodewise
(xyz)Computes relative position of xyz on lines from pial to white matter. surf_unproject_weights_nodewise
(weights)Maps relative positions in grey matter to coordinates Parameters: volgeom: volgeom.VolGeom
Volume geometry
white: surf.Surface
Surface representing whitegrey matter boundary
pial: surf.Surface
Surface representing pialgrey matter boundary
intermediate: surf.Surface (default: None).
Surface representing intermediate surface. If omitted it is the nodewise average of white and pial. This parameter is usually ignored, except when used in a VolSurfMinimalLowresMapping.
Notes
‘pial’ and ‘white’ should have the same topology.
Attributes
intermediate_surface
Returns the nodewise average of the pial and white surface pial_surface
Returns the pial surface volgeom
Returns the volume geometry white_surface
Returns the white surface Methods
coordinates_to_grey_distance_mm
(nodes, xyz)Computes the grey position of coordinates in metric units surf_project_nodewise
(xyz)Projects coordinates on lines connecting pial and white matter. surf_project_weights
(nodes, xyz)Computes relative position of xyz on lines from pial to white matter. surf_project_weights_nodewise
(xyz)Computes relative position of xyz on lines from pial to white matter. surf_unproject_weights_nodewise
(weights)Maps relative positions in grey matter to coordinates 
coordinates_to_grey_distance_mm
(nodes, xyz)¶ Computes the grey position of coordinates in metric units
Parameters: nodes: int or np.ndarray
Single index, or Q indices of nodes relative to which the coordinates are computed. If True then grey distances are computed nodewise.
xyz: Px3 array with coordinates, assuming ‘white’ and ‘pial’ surfaces
have P nodes each.
Returns: grey_position_mm: np.ndarray
Vector with P elements (if type(nodes) is int) or PxQ array (with type(nodes) is np.ndarray) containing the signed ‘distance’ to the grey matter. Values of zero indicate a node is within the grey matter. Negative values indicate that a node is ‘below’ the white matter (i.e. farther from the pial surface than the white surface), whereas Positive values indicate that a node is ‘above’ the pial matter.

intermediate_surface
¶ Returns the nodewise average of the pial and white surface
Returns: intermediate: surf.Surface

pial_surface
¶ Returns the pial surface
Returns: pial: surf.Surface

surf_project_nodewise
(xyz)¶ Projects coordinates on lines connecting pial and white matter.
Parameters: xyz: numpy.ndarray (float)
Px3 array with coordinates, assuming ‘white’ and ‘pial’ surfaces have P nodes each
Returns: xyz_proj: numpy.ndarray (float)
Px3 array with coordinates the constraints that xyz_proj[i,:] lies on the line connecting node ‘i’ on the white and pial surface, and that xyz_proj[i,:] is closest to xyz[i,:] of all points on this line.

surf_project_weights
(nodes, xyz)¶ Computes relative position of xyz on lines from pial to white matter.
Parameters: nodes: True or np.ndarray or int
Q node indices for each the weights are computed. If True, then weights are computed nodewise, otherwise separately for each node.
xyz: numpy.ndarray (float)
Px3 array with coordinates. IF nodes is True then the ‘white’ and ‘pial’ surfaces must have P nodes each.
Returns: weights: numpy.ndarray (float)
If nodes is True, P values of relative grey matter positions (0=white surface and 1=pial surface), where the ith element are the projection weights for xyz[i] relative to the ith node in the pial and white surface. Otherwise it returns an PxQ array with the projected weights for each node. If nodes is an int, then a Pvector is returned

surf_project_weights_nodewise
(xyz)¶ Computes relative position of xyz on lines from pial to white matter.
Parameters: xyz: numpy.ndarray (float)
Px3 array with coordinates, assuming ‘white’ and ‘pial’ surfaces have P nodes each.
Returns: weights: numpy.ndarray (float)
If nodes is True, P values of relative grey matter positions (0=white surface and 1=pial surface), where the ith element are the projection weights for xyz[i] relative to the ith node in the pial and white surface. Otherwise it returns an PxQ array with the projected weights for each node. If nodes is an int, then a Pvector is returned

surf_unproject_weights_nodewise
(weights)¶ Maps relative positions in grey matter to coordinates
Parameters: weights: numpy.ndarray (float)
P values of relative grey matter positions, where 0=white surface and 1=pial surface.
Returns: xyz: numpy.ndarray (float)
Px3 array with coordinates, assuming ‘white’ and ‘pial’ surfaces have P nodes each.

volgeom
¶ Returns the volume geometry
Returns: vg: volgeom.VolGeom

white_surface
¶ Returns the white surface
Returns: white: surf.Surface
