nipy.labs.viz_tools.maps_3d.plot_map_3d

nipy.labs.viz_tools.maps_3d.plot_map_3d(map, affine, cut_coords=None, anat=None, anat_affine=None, threshold=None, offscreen=False, vmin=None, vmax=None, cmap=None, view=(38.5, 70.5, 300, (-2.7, -12, 9.1)))

Plot a 3D volume rendering view of the activation, with an outline of the brain.

Parameters:

map : 3D ndarray

The activation map, as a 3D image.

affine : 4x4 ndarray

The affine matrix going from image voxel space to MNI space.

cut_coords: 3-tuple of floats, optional

The MNI coordinates of a 3D cursor to indicate a feature or a cut, in MNI coordinates and order.

anat : 3D ndarray, optional

The anatomical image to be used as a background. If None, the MNI152 T1 1mm template is used. If False, no anatomical image is used.

anat_affine : 4x4 ndarray, optional

The affine matrix going from the anatomical image voxel space to MNI space. This parameter is not used when the default anatomical is used, but it is compulsory when using an explicite anatomical image.

threshold : float, optional

The lower threshold of the positive activation. This parameter is used to threshold the activation map.

offscreen: boolean, optional

If True, Mayavi attempts to plot offscreen. Will work only with VTK >= 5.2.

vmin : float, optional

The minimal value, for the colormap

vmax : float, optional

The maximum value, for the colormap

cmap : a callable, or a pylab colormap

A callable returning a (n, 4) array for n values between 0 and 1 for the colors. This can be for instance a pylab colormap.

Notes

If you are using a VTK version below 5.2, there is no way to avoid opening a window during the rendering under Linux. This is necessary to use the graphics card for the rendering. You must maintain this window on top of others and on the screen.