mne.viz.plot_alignment¶
- mne.viz.plot_alignment(info=None, trans=None, subject=None, subjects_dir=None, surfaces='auto', coord_frame='head', meg=None, eeg='original', fwd=None, dig=False, ecog=True, src=None, mri_fiducials=False, bem=None, seeg=True, fnirs=True, show_axes=False, dbs=True, fig=None, interaction='trackball', verbose=None)[source]¶
Plot head, sensor, and source space alignment in 3D.
- Parameters
- info
dict
|None
The measurement info. If None (default), no sensor information will be shown.
- trans
str
|dict
| instance ofTransform
|None
If str, the path to the head<->MRI transform
*-trans.fif
file produced during coregistration. Can also be'fsaverage'
to use the built-in fsaverage transformation. If trans is None, an identity matrix is assumed.Changed in version 0.19: Support for ‘fsaverage’ argument.
- 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
|dict
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’).
Can be dict to specify alpha values for each surface. Use None to specify default value. Specified values must be between 0 and 1. for example:
surfaces=dict(brain=0.4, outer_skull=0.6, head=None)
Defaults to ‘auto’, which will look for a head surface and plot it if found.
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')
.- eegbool |
str
|list
String options are:
- “original” (default; equivalent to
True
) Shows EEG sensors using their digitized locations (after transformation to the chosen
coord_frame
)
- “original” (default; equivalent to
- “projected”
The EEG locations projected onto the scalp, as is done in forward modeling
Can also be a list of these options, or an empty list (
[]
, equivalent ofFalse
).- fwdinstance of
Forward
The forward solution. If present, the orientations of the dipoles present in the forward solution are displayed.
- 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
). Ifstr
, it can be'estimated'
to usemne.coreg.get_mni_fiducials()
, otherwise it should provide the full path to the fiducials file.New in version 0.22: Support for
'estimated'
.- bem
list
ofdict
| instance ofConductorModel
|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.
- fnirs
str
|list
| bool |None
Can be “channels”, “pairs”, “detectors”, and/or “sources” to show the fNIRS channel locations, optode locations, or line between source-detector pairs, or a combination like
('pairs', 'channels')
. True translates to('pairs',)
.New in version 0.20.
- 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.
- dbsbool
If True (default), show DBS (deep brain stimulation) electrodes.
- fig
mayavi.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.
- interaction
str
Can be “trackball” (default) or “terrain”, i.e. a turntable-style camera.
New in version 0.16.
- verbosebool,
str
,int
, orNone
If not None, override default verbose level (see
mne.verbose()
and Logging documentation for more). If used, it should be passed as a keyword-argument only.
- info
- Returns
- figinstance of
mayavi.mlab.Figure
The mayavi figure.
- figinstance of
See also
Notes
This function serves the purpose of checking the validity of the many different steps of source reconstruction:
Transform matrix (keywords
trans
,meg
andmri_fiducials
),BEM surfaces (keywords
bem
andsurfaces
),sphere conductor model (keywords
bem
andsurfaces
) andsource space (keywords
surfaces
andsrc
).
New in version 0.15.