mne.coreg.Coregistration¶
- class mne.coreg.Coregistration(info, subject, subjects_dir=None, fiducials='auto')[source]¶
Class for MRI<->head coregistration.
- Parameters
- infoinstance of
Info
|None
The measurement info.
- subject
str
The FreeSurfer subject name.
- subjects_dir
str
|pathlib.Path
|None
The path to the directory containing the FreeSurfer subjects reconstructions. If
None
, defaults to theSUBJECTS_DIR
environment variable.- fiducials
list
|dict
|str
The fiducials given in the MRI (surface RAS) coordinate system. If a dict is provided it must be a dict with 3 entries with keys ‘lpa’, ‘rpa’ and ‘nasion’ with as values coordinates in m. If a list it must be a list of DigPoint instances as returned by the read_fiducials function. If set to ‘estimated’, the fiducials are initialized automatically using fiducials defined in MNI space on fsaverage template. If set to ‘auto’, one tries to find the fiducials in a file with the canonical name (
bem/{subject}-fiducials.fif
) and if abstent one falls back to ‘estimated’. Defaults to ‘auto’.
- infoinstance of
See also
Notes
Internal computation quantities parameters are in the following units:
rotation are in radians
translation are in m
scale are in scale proportion
If using a scale mode, the
scale_mri()
should be used to create a surrogate MRI subject with the proper scale factors.Methods
__hash__
(/)Return hash(self).
Compute distance between head shape points and MRI skin surface.
fit_fiducials
([lpa_weight, nasion_weight, ...])Find rotation and translation to fit all 3 fiducials.
fit_icp
([n_iterations, lpa_weight, ...])Find MRI scaling, translation, and rotation to match HSP.
omit_head_shape_points
(distance)Exclude head shape points that are far away from the MRI head.
reset
()Reset all the parameters affecting the coregistration.
set_fid_match
(match)Set the strategy for fitting anatomical landmark (fiducial) points.
set_grow_hair
(value)Compensate for hair on the digitizer head shape.
set_rotation
(rot)Set the rotation parameter.
set_scale
(sca)Set the scale parameter.
set_scale_mode
(scale_mode)Select how to fit the scale parameters.
set_translation
(tra)Set the translation parameter.
- compute_dig_mri_distances()[source]¶
Compute distance between head shape points and MRI skin surface.
- Returns
- dist
array
, shape (n_points,) The distance of the head shape points to the MRI skin surface.
- dist
See also
Examples using
compute_dig_mri_distances
:
- fit_fiducials(lpa_weight=1.0, nasion_weight=10.0, rpa_weight=1.0, verbose=None)[source]¶
Find rotation and translation to fit all 3 fiducials.
- Parameters
- lpa_weight
float
Relative weight for LPA. The default value is 1.
- nasion_weight
float
Relative weight for nasion. The default value is 10.
- rpa_weight
float
Relative weight for RPA. The default value is 1.
- verbosebool |
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.
- lpa_weight
- Returns
- self
Coregistration
The modified Coregistration object.
- self
Examples using
fit_fiducials
:
- fit_icp(n_iterations=20, lpa_weight=1.0, nasion_weight=10.0, rpa_weight=1.0, hsp_weight=1.0, eeg_weight=1.0, hpi_weight=1.0, callback=None, verbose=None)[source]¶
Find MRI scaling, translation, and rotation to match HSP.
- Parameters
- n_iterations
int
Maximum number of iterations.
- lpa_weight
float
Relative weight for LPA. The default value is 1.
- nasion_weight
float
Relative weight for nasion. The default value is 10.
- rpa_weight
float
Relative weight for RPA. The default value is 1.
- hsp_weight
float
Relative weight for HSP. The default value is 1.
- eeg_weight
float
Relative weight for EEG. The default value is 1.
- hpi_weight
float
Relative weight for HPI. The default value is 1.
- callback
callable()
|None
A function to call on each iteration. Useful for status message updates. It will be passed the keyword arguments
iteration
andn_iterations
.- verbosebool |
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.
- n_iterations
- Returns
- self
Coregistration
The modified Coregistration object.
- self
Examples using
fit_icp
:
- omit_head_shape_points(distance)[source]¶
Exclude head shape points that are far away from the MRI head.
- Parameters
- distance
float
Exclude all points that are further away from the MRI head than this distance (in m.). A value of distance <= 0 excludes nothing.
- distance
- Returns
- self
Coregistration
The modified Coregistration object.
- self
Examples using
omit_head_shape_points
:
- reset()[source]¶
Reset all the parameters affecting the coregistration.
- Returns
- self
Coregistration
The modified Coregistration object.
- self
- set_fid_match(match)[source]¶
Set the strategy for fitting anatomical landmark (fiducial) points.
- Parameters
- match‘nearest’ | ‘matched’
Alignment strategy;
'nearest'
aligns anatomical landmarks to any point on the head surface;'matched'
aligns to the fiducial points in the MRI.
- Returns
- self
Coregistration
The modified Coregistration object.
- self
- set_grow_hair(value)[source]¶
Compensate for hair on the digitizer head shape.
- Parameters
- value
float
Move the back of the MRI head outwards by
value
(mm).
- value
- Returns
- self
Coregistration
The modified Coregistration object.
- self
- set_rotation(rot)[source]¶
Set the rotation parameter.
- Parameters
- rot
array
, shape (3,) The rotation parameter (in radians).
- rot
- Returns
- self
Coregistration
The modified Coregistration object.
- self
- set_scale(sca)[source]¶
Set the scale parameter.
- Parameters
- sca
array
, shape (3,) The scale parameter.
- sca
- Returns
- self
Coregistration
The modified Coregistration object.
- self
- set_scale_mode(scale_mode)[source]¶
Select how to fit the scale parameters.
- Parameters
- Returns
- self
Coregistration
The modified Coregistration object.
- self
Examples using
set_scale_mode
:
- set_translation(tra)[source]¶
Set the translation parameter.
- Parameters
- tra
array
, shape (3,) The translation parameter (in m.).
- tra
- Returns
- self
Coregistration
The modified Coregistration object.
- self
- property trans¶
Return the head-mri transform.