- 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)¶
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.
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_pathparameter for details.
The path of the electrophysiology recording. If
suffixare not present, they will be set to
'meg', and a warning will be raised.
Changed in version 0.10: A warning is raised it
suffixare not set.
Extra parameters to be passed to
mne.io.read_raw()when reading the MEG file.
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_pathparameter. Alternatively, you explicitly specify which T1-weighted MRI scan to use for extraction of MRI landmarks. To do that, pass a
mne_bids.BIDSPathpointing 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.
The subject identifier used for FreeSurfer.
Changed in version 0.10: Does not default anymore to
- fs_subjects_dirpath-like |
The FreeSurfer subjects directory. If
None, defaults to the
New in version 0.8.
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
NAS_ses-1, you should pass
None, no suffix is appended, the landmarks named
RPAwill be used.
New in version 0.10.
The data transformation matrix from head to MRI coordinates.