mne.coreg.get_mni_fiducials#
- mne.coreg.get_mni_fiducials(subject, subjects_dir=None, verbose=None)[source]#
Estimate fiducials for a subject.
- Parameters:
- subject
str
The FreeSurfer subject name.
- subjects_dirpath-like |
None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- verbose
bool
|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.
- subject
- Returns:
- fids_mri
list
List of estimated fiducials (each point in a dict), in the order LPA, nasion, RPA.
- fids_mri
Notes
This takes the
fsaverage-fiducials.fif
file included with MNE—which contain the LPA, nasion, and RPA for thefsaverage
subject—and transforms them to the given FreeSurfer subject’s MRI space. The MRI offsaverage
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