mne_bids.get_head_mri_trans#

mne_bids.get_head_mri_trans(bids_path, extra_params=None, t1_bids_path=None, fs_subject=None, fs_subjects_dir=None, *, kind=None, verbose=None)[source]#

Produce transformation matrix from MEG and MRI landmark points.

Will attempt to read the landmarks of Nasion, LPA, and RPA from the sidecar files of (i) the MEG and (ii) the T1-weighted MRI data. The two sets of points will then be used to calculate a transformation matrix from head coordinates to MRI coordinates.

Note

The MEG and MRI data need not necessarily be stored in the same session or even in the same BIDS dataset. See the t1_bids_path parameter for details.

Parameters:
bids_pathBIDSPath

The path of the electrophysiology recording. If datatype and suffix are not present, they will be set to 'meg', and a warning will be raised.

Changed in version 0.10: A warning is raised it datatype or suffix are not set.

extra_paramsNone | dict

Extra parameters to be passed to mne.io.read_raw() when reading the MEG file.

t1_bids_pathBIDSPath | None

If None (default), will try to discover the T1-weighted MRI file based on the name and location of the MEG recording specified via the bids_path parameter. Alternatively, you explicitly specify which T1-weighted MRI scan to use for extraction of MRI landmarks. To do that, pass a mne_bids.BIDSPath pointing to the scan. Use this parameter e.g. if the T1 scan was recorded during a different session than the MEG. It is even possible to point to a T1 image stored in an entirely different BIDS dataset than the MEG data.

fs_subjectstr

The subject identifier used for FreeSurfer.

Changed in version 0.10: Does not default anymore to bids_path.subject if None.

fs_subjects_dirpath-like | None

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

Added in version 0.8.

kindstr | None

The suffix of the anatomical landmark names in the JSON sidecar. A suffix might be present e.g. to distinguish landmarks between sessions. If provided, should not include a leading underscore _. For example, if the landmark names in the JSON sidecar file are LPA_ses-1, RPA_ses-1, NAS_ses-1, you should pass 'ses-1' here. If None, no suffix is appended, the landmarks named Nasion (or NAS), LPA, and RPA will be used.

Added in version 0.10.

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:
transmne.transforms.Transform

The data transformation matrix from head to MRI coordinates.

Examples using mne_bids.get_head_mri_trans#

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

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