niwidgets.SurfaceWidget

class niwidgets.SurfaceWidget(meshfile, overlayfiles=())

Interact with brain surfaces right in the notebook.

---

Methods

Surface widget methods:

---

Methods Details

class niwidgets.SurfaceWidget(meshfile, overlayfiles=())

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)

Visualise a surface mesh (with overlay) inside notebooks.

This method displays the surface widget.

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(mask)

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.