mne.gui.coregistration#
- mne.gui.coregistration(*, width=None, height=None, inst=None, subject=None, subjects_dir=None, head_opacity=None, head_high_res=None, trans=None, orient_to_surface=None, scale_by_distance=None, mark_inside=None, interaction=None, fullscreen=None, show=True, block=False, verbose=None)[source]#
Coregister an MRI with a subject’s head shape.
The GUI can be launched through the command line interface:
$ mne coreg
or using a python interpreter as shown in Source alignment and coordinate frames.
- Parameters:
- width
int
|None
Specify the width for window (in logical pixels). Default is None, which uses
MNE_COREG_WINDOW_WIDTH
config value (which defaults to800
).- height
int
|None
Specify a height for window (in logical pixels). Default is None, which uses
MNE_COREG_WINDOW_WIDTH
config value (which defaults to400
).- inst
None
| path-like Path to an instance file containing the digitizer data. Compatible for Raw, Epochs, and Evoked files.
- subject
None
|str
Name of the mri subject.
- subjects_dirpath-like |
None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- head_opacity
float
|None
The opacity of the head surface in the range
[0., 1.]
. Default is None, which usesMNE_COREG_HEAD_OPACITY
config value (which defaults to1.
).- head_high_resbool |
None
Use a high resolution head surface. Default is None, which uses
MNE_COREG_HEAD_HIGH_RES
config value (which defaults to True).- transpath-like |
Transform
|None
The Head<->MRI transform or the path to its FIF file (
"-trans.fif"
).- orient_to_surfacebool |
None
If True (default), orient EEG electrode and head shape points to the head surface.
New in v0.16.
- scale_by_distancebool |
None
If True (default), scale the digitization points by their distance from the scalp surface.
New in v0.16.
- mark_insidebool |
None
If True (default), mark points inside the head surface in a different color.
New in v0.16.
- interaction‘trackball’ | ‘terrain’ |
None
How interactions with the scene via an input device (e.g., mouse or trackpad) modify the camera position. If
'terrain'
, one axis is fixed, enabling “turntable-style” rotations. If'trackball'
, movement along all axes is possible, which provides more freedom of movement, but you may incidentally perform unintentional rotations along some axes. IfNone
, the setting stored in the MNE-Python configuration file is used. Defaults to'terrain'
.New in v0.16.
Changed in version 1.0: Default interaction mode if
None
and no config setting found changed from'trackball'
to'terrain'
.- fullscreenbool
Whether to start in fullscreen (
True
) or windowed mode (False
). Default isNone
, which usesMNE_COREG_FULLSCREEN
config value (which defaults toFalse
).New in v1.1.
- showbool
Show the GUI if True.
- blockbool
Whether to halt program execution until the figure is closed.
- verbosebool |
str
|int
|None
Control verbosity of the logging output. If
None
, use the default verbosity level. See the logging documentation andmne.verbose()
for details. Should only be passed as a keyword argument.
- width
- Returns:
- frameinstance of CoregistrationUI
The coregistration frame.
Notes
Many parameters (e.g.,
head_opacity
) take None as a parameter, which means that the default will be read from the MNE-Python configuration file (which gets saved when exiting).Step by step instructions for the coregistrations are shown below:
Examples using mne.gui.coregistration
#
Source alignment and coordinate frames