mne.viz.plot_alignment

mne.viz.plot_alignment(info=None, 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
infodict | None

The measurement info. If None (default), no sensor information will be shown.

transstr | ‘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.

subjectstr | None

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

subjects_dirstr | None

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

surfacesstr | 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_framestr

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

megstr | 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').

eegbool | 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).

digbool | ‘fiducials’

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

ecogbool

If True (default), show ECoG sensors.

srcinstance of SourceSpaces | None

If not None, also plot the source space points.

mri_fiducialsbool | 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.

bemlist 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.

seegbool

If True (default), show sEEG electrodes.

show_axesbool

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.

figmayavi.mlab.Figure | None

Mayavi Scene in which to plot the alignment. If None, creates a new 600x600 pixel figure with black background.

New in version 0.16.

interactionstr

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

New in version 0.16.

verbosebool, str, int, or None

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

Returns
figinstance of mayavi.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.