mne.gui.coregistration¶

mne.gui.coregistration(tabbed=False, split=True, width=None, inst=None, subject=None, subjects_dir=None, guess_mri_subject=None, height=None, head_opacity=None, head_high_res=None, trans=None, scrollable=True, project_eeg=None, orient_to_surface=None, scale_by_distance=None, mark_inside=None, interaction=None, scale=None, advanced_rendering=None, verbose=None)[source]¶

Coregister an MRI with a subject’s head shape.

The recommended way to use the GUI is through bash with:

$ mne coreg

Parameters

tabbedbool: Combine the data source panel and the coregistration panel into a single panel with tabs.
splitbool: Split the main panels with a movable splitter (good for QT4 but unnecessary for wx backend).
widthint | None: Specify the width for window (in logical pixels). Default is None, which uses MNE_COREG_WINDOW_WIDTH config value (which defaults to 800).
instNone | str: Path to an instance file containing the digitizer data. Compatible for Raw, Epochs, and Evoked files.
subjectNone | str: Name of the mri subject.
subjects_dirstr | None: The path to the FreeSurfer subjects reconstructions. It corresponds to FreeSurfer environment variable SUBJECTS_DIR.
guess_mri_subjectbool: When selecting a new head shape file, guess the subject’s name based on the filename and change the MRI subject accordingly (default True).
heightint | None: Specify a height for window (in logical pixels). Default is None, which uses MNE_COREG_WINDOW_WIDTH config value (which defaults to 400).
head_opacityfloat | None: The opacity of the head surface in the range [0., 1.]. Default is None, which uses MNE_COREG_HEAD_OPACITY config value (which defaults to 1.).
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).
transstr | None: The transform file to use.
scrollablebool: Make the coregistration panel vertically scrollable (default True).
project_eegbool | None: If True (default None), project EEG electrodes to the head surface. This is only for visualization purposes and does not affect fitting.

New in version 0.16.
orient_to_surfacebool | None: If True (default None), orient EEG electrode and head shape points to the head surface.

New in version 0.16.
scale_by_distancebool | None: If True (default None), scale the digitization points by their distance from the scalp surface.

New in version 0.16.
mark_insidebool | None: If True (default None), mark points inside the head surface in a different color.

New in version 0.16.
interactionstr | None: Can be ‘terrain’ (default None), use terrain-style interaction (where “up” is the Z/superior direction), or ‘trackball’ to use orientationless interactions.

New in version 0.16.
scalefloat | None: The scaling for the scene.

New in version 0.16.
advanced_renderingbool: Use advanced OpenGL rendering techniques (default True). For some renderers (such as MESA software) this can cause rendering bugs.

New in version 0.18.
verbosebool, str, int, or None: 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.

Returns

frameinstance of CoregFrame: The coregistration frame.

Notes

Many parameters (e.g., project_eeg) 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 can be accessed as slides, for subjects with structural MRI and for subjects for which no MRI is available.