Function get_mni_fiducials

mne/_freesurfer.py:432–477

Estimate fiducials for a subject. Parameters ---------- %(subject)s %(subjects_dir)s %(verbose)s Returns ------- fids_mri : list List of estimated fiducials (each point in a dict), in the order LPA, nasion, RPA. Notes ----- This takes th

(subject, subjects_dir=None, verbose=None)

@verbose
def get_mni_fiducials(subject, subjects_dir=None, verbose=None):
    """Estimate fiducials for a subject.

    Parameters
    ----------
    %(subject)s
    %(subjects_dir)s
    %(verbose)s

    Returns
    -------
    fids_mri : list
        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
    :ref:`tut-source-alignment`.
    """
    # Eventually we might want to allow using the MNI Talairach with-skull
    # transformation rather than the standard brain-based MNI Talaranch
    # transformation, and/or project the points onto the head surface
    # (if available).
    fname_fids_fs = (
        Path(__file__).parent / "data" / "fsaverage" / "fsaverage-fiducials.fif"
    )

    # Read fsaverage fiducials file and subject Talairach.
    fids, coord_frame = read_fiducials(fname_fids_fs)
    assert coord_frame == FIFF.FIFFV_COORD_MRI
    if subject == "fsaverage":
        return fids  # special short-circuit for fsaverage
    mni_mri_t = invert_transform(read_talxfm(subject, subjects_dir))
    for f in fids:
        f["r"] = apply_trans(mni_mri_t, f["r"])
    return fids


@verbose