mne.coreg.get_mni_fiducials#

mne.coreg.get_mni_fiducials(subject, subjects_dir=None, verbose=None)[source]#

Estimate fiducials for a subject.

Parameters:

subjectstr

The FreeSurfer subject name.

subjects_dirpath-like | None

The path to the directory containing the FreeSurfer subjects reconstructions. If None, defaults to the SUBJECTS_DIR environment variable.

verbosebool | str | int | None

Control verbosity of the logging output. If None, use the default verbosity level. See the logging documentation and mne.verbose() for details. Should only be passed as a keyword argument.

Returns:

fids_mrilist

List of estimated fiducials (each point in a dict), in the order LPA, nasion, RPA.

Notes

This takes the fsaverage-fiducials.fif file included with MNE—which contain the LPA, nasion, and RPA for the fsaverage subject—and transforms them to the given FreeSurfer subject’s MRI space. The MRI of fsaverage is already in MNI Talairach space, so applying the inverse of the given subject’s MNI Talairach affine transformation ($SUBJECTS_DIR/$SUBJECT/mri/transforms/talairach.xfm) is used to estimate the subject’s fiducial locations.

For more details about the coordinate systems and transformations involved, see https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems and Source alignment and coordinate frames.

Examples using mne.coreg.get_mni_fiducials#

How MNE uses FreeSurfer’s outputs

How MNE uses FreeSurfer's outputs

Locating intracranial electrode contacts

Locating intracranial electrode contacts