BEM surface
use_template_mri
module-attribute
¶
use_template_mri: str | None = None
Whether to use a template MRI subject such as FreeSurfer's fsaverage
subject.
This may come in handy if you don't have individual MR scans of your
participants, as is often the case in EEG studies.
Note that the template MRI subject must be available as a subject
in your subjects_dir. You can use for example a scaled version
of fsaverage that could get with
mne.scale_mri
.
Scaling fsaverage can be a solution to problems that occur when the head of a
subject is small compared to fsaverage
and, therefore, the default
coregistration mislocalizes MEG sensors inside the head.
Example
use_template_mri = "fsaverage"
Pipeline steps using this setting
The following steps are directly affected by changes to
use_template_mri
:
source/_01_make_bem_surfaces
source/_02_make_bem_solution
source/_03_setup_source_space
source/_04_make_forward
source/_05_make_inverse
source/_99_group_average
freesurfer/_02_coreg_surfaces
adjust_coreg
module-attribute
¶
adjust_coreg: bool = False
Whether to adjust the coregistration between the MRI and the channels
locations, possibly combined with the digitized head shape points.
Setting it to True is mandatory if you use a template MRI subject
that is different from fsaverage
.
Example
adjust_coreg = True
Pipeline steps using this setting
The following steps are directly affected by changes to
adjust_coreg
:
source/_04_make_forward
bem_mri_images
module-attribute
¶
bem_mri_images: Literal['FLASH', 'T1', 'auto'] = 'auto'
Which types of MRI images to use when creating the BEM model.
If 'FLASH'
, use FLASH MRI images, and raise an exception if they cannot be
found.
Advice
It is recommended to use the FLASH images if available, as the quality of the extracted BEM surfaces will be higher.
If 'T1'
, create the BEM surfaces from the T1-weighted images using the
watershed
algorithm.
If 'auto'
, use FLASH images if available, and use the `watershed``
algorithm with the T1-weighted images otherwise.
Pipeline steps using this setting
The following steps are directly affected by changes to
bem_mri_images
:
source/_01_make_bem_surfaces
recreate_bem
module-attribute
¶
recreate_bem: bool = False
Whether to re-create the BEM surfaces, even if existing surfaces have been
found. If False
, the BEM surfaces are only created if they do not exist
already. True
forces their recreation, overwriting existing BEM surfaces.
Pipeline steps using this setting
The following steps are directly affected by changes to
recreate_bem
:
source/_01_make_bem_surfaces
source/_02_make_bem_solution
recreate_scalp_surface
module-attribute
¶
recreate_scalp_surface: bool = False
Whether to re-create the scalp surfaces used for visualization of the
coregistration in the report and the lower-density coregistration surfaces.
If False
, the scalp surface is only created if it does not exist already.
If True
, forces a re-computation.
Pipeline steps using this setting
The following steps are directly affected by changes to
recreate_scalp_surface
:
freesurfer/_02_coreg_surfaces
freesurfer_verbose
module-attribute
¶
freesurfer_verbose: bool = False
Whether to print the complete output of FreeSurfer commands. Note that if
False
, no FreeSurfer output might be displayed at all!
Pipeline steps using this setting
The following steps are directly affected by changes to
freesurfer_verbose
:
source/_01_make_bem_surfaces