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.

map3D ndarray

The activation map, as a 3D image.

affine4x4 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.

anat3D 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_affine4x4 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.

thresholdfloat, 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.

vminfloat, optional

The minimal value, for the colormap

vmaxfloat, optional

The maximum value, for the colormap

cmapa 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.


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.