mne.viz.plot_alignment

mne.viz.plot_alignment(info, trans=None, subject=None, subjects_dir=None, surfaces='head', coord_frame='head', meg=None, eeg='original', dig=False, ecog=True, src=None, mri_fiducials=False, bem=None, seeg=True, show_axes=False, fig=None, interaction='trackball', verbose=None)[source]

Plot head, sensor, and source space alignment in 3D.

Parameters:
info : dict

The measurement info.

trans : str | ‘auto’ | dict | None

The full path to the head<->MRI transform *-trans.fif file produced during coregistration. If trans is None, an identity matrix is assumed.

subject : str | None

The subject name corresponding to FreeSurfer environment variable SUBJECT. Can be omitted if src is provided.

subjects_dir : str | None

The path to the freesurfer subjects reconstructions. It corresponds to Freesurfer environment variable SUBJECTS_DIR.

surfaces : str | list

Surfaces to plot. Supported values:

  • scalp: one of ‘head’, ‘outer_skin’ (alias for ‘head’), ‘head-dense’, or ‘seghead’ (alias for ‘head-dense’)
  • skull: ‘outer_skull’, ‘inner_skull’, ‘brain’ (alias for ‘inner_skull’)
  • brain: one of ‘pial’, ‘white’, ‘inflated’, or ‘brain’ (alias for ‘pial’).

Defaults to ‘head’.

Note

For single layer BEMs it is recommended to use ‘brain’.

coord_frame : str

Coordinate frame to use, ‘head’, ‘meg’, or ‘mri’.

meg : str | list | bool | None

Can be “helmet”, “sensors” or “ref” to show the MEG helmet, sensors or reference sensors respectively, or a combination like ('helmet', 'sensors') (same as None, default). True translates to ('helmet', 'sensors', 'ref').

eeg : bool | str | list

Can be “original” (default; equivalent to True) or “projected” to show EEG sensors in their digitized locations or projected onto the scalp, or a list of these options including [] (equivalent of False).

dig : bool | ‘fiducials’

If True, plot the digitization points; ‘fiducials’ to plot fiducial points only.

ecog : bool

If True (default), show ECoG sensors.

src : instance of SourceSpaces | None

If not None, also plot the source space points.

mri_fiducials : bool | str

Plot MRI fiducials (default False). If True, look for a file with the canonical name (bem/{subject}-fiducials.fif). If str it should provide the full path to the fiducials file.

bem : list of dict | Instance of ConductorModel | None

Can be either the BEM surfaces (list of dict), a BEM solution or a sphere model. If None, we first try loading ‘$SUBJECTS_DIR/$SUBJECT/bem/$SUBJECT-$SOURCE.fif’, and then look for ‘$SUBJECT*$SOURCE.fif’ in the same directory. For ‘outer_skin’, the subjects bem and bem/flash folders are searched. Defaults to None.

seeg : bool

If True (default), show sEEG electrodes.

show_axes : bool

If True (default False), coordinate frame axis indicators will be shown:

  • head in pink
  • MRI in gray (if trans is not None)
  • MEG in blue (if MEG sensors are present)

New in version 0.16.

fig : mayavi figure object | None

Mayavi Scene (instance of mlab.Figure) in which to plot the alignment. If None, creates a new 600x600 pixel figure with black background.

New in version 0.16.

interaction : str

Can be “trackball” (default) or “terrain”, i.e. a turntable-style camera.

New in version 0.16.

verbose : bool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more).

Returns:
fig : instance of mlab.Figure

The mayavi figure.

See also

mne.viz.plot_bem

Notes

This function serves the purpose of checking the validity of the many different steps of source reconstruction:

  • Transform matrix (keywords trans, meg and mri_fiducials),
  • BEM surfaces (keywords bem and surfaces),
  • sphere conductor model (keywords bem and surfaces) and
  • source space (keywords surfaces and src).

New in version 0.15.