niwidgets.SurfaceWidget

class niwidgets.SurfaceWidget(meshfile, overlayfiles=[])[source]

Interact with brain surfaces right in the notebook.


Methods

These are the methods that are added by niwidgets. All methods, including the inherited ones, are at the end of the page.

surface_plotter([colormap, figsize, …]) Visualise a surface mesh (with overlay) inside notebooks.
zmask(surf, mask) Masks out vertices with intensity=0 from overlay.

Methods Details

class niwidgets.SurfaceWidget(meshfile, overlayfiles=[])[source]

Interact with brain surfaces right in the notebook.

surface_plotter(colormap=None, figsize=array([600, 600]), figlims=array([[-100, 100], [-100, 100], [-100, 100]]), show_zeroes=True, **kwargs)[source]

Visualise a surface mesh (with overlay) inside notebooks.

Basic functionality: Read mesh and overlay data Setup the interactive widget Set defaults for plotting

Parameters:
  • surface (str, gifti object) – Path to surface file in gifti or FS surface format or an already loaded gifti object of surface
  • overlay (str, gifti object) – Path to overlay file in gifti or FS annot or anatomical (.curv,.sulc,.thickness) format or an already loaded gifti object of overlay, default None
  • colormap (string) – A matplotlib colormap, default summer
  • figsize (ndarray) – Size of the figure to display, default [600,600]
  • figlims (ndarray) – x,y and z limits of the axes, default [[-100,100],[-100,100],[-100,100]]
  • show_zeroes (bool) – Display vertices with intensity = 0, default True
zmask(surf, mask)[source]

Masks out vertices with intensity=0 from overlay.

Also returns masked-out vertices.

Parameters:
  • surf (gifti object) – already loaded gifti object of target surface
  • mask (gifti object) – already loaded gifti object of overlay with zeroes at vertices of no interest (e.g. medial wall)
Returns:

  • mask_keep (np.ndarray) – Boolean array of what to show.
  • mask_kill (np.ndarray) – Boolean array of what to hide.