mne_bids.get_anat_landmarks#

mne_bids.get_anat_landmarks(image, info, trans, fs_subject, fs_subjects_dir=None)[source]#

Get anatomical landmarks in MRI voxel coordinates.

This function transforms the fiducial points from “head” to MRI “voxel” coordinate space. The landmarks obtained are defined w.r.t. the MRI passed via the image parameter.

Parameters:
imagepath-like | mne_bids.BIDSPath | NibabelImageObject

Path to an MRI scan (e.g. T1w) of the subject. Can be in any format readable by nibabel. Can also be a nibabel image object of an MRI scan. Will be written as a .nii.gz file.

infomne.Info

The measurement information from an electrophysiology recording of the subject with the anatomical landmarks stored in its mne.channels.DigMontage.

transmne.transforms.Transform | path-like

The transformation matrix from head to MRI coordinates. Can also be a string pointing to a .trans file containing the transformation matrix.

fs_subjectstr

The subject identifier used for FreeSurfer. Must be provided to write the anatomical landmarks if they are not provided in MRI voxel space. This is because the head coordinate of a mne.channels.DigMontage is aligned using FreeSurfer surfaces.

fs_subjects_dirpath-like | None

The FreeSurfer subjects directory. If None, defaults to the SUBJECTS_DIR environment variable. Must be provided to write anatomical landmarks if they are not provided in MRI voxel space.

Returns:
landmarksmne.channels.DigMontage

A montage with the landmarks in MRI voxel space.

Examples using mne_bids.get_anat_landmarks#

Convert iEEG data to BIDS format

Convert iEEG data to BIDS format

Save and load T1-weighted MRI scan along with anatomical landmarks in BIDS

Save and load T1-weighted MRI scan along with anatomical landmarks in BIDS