meegpype.interfaces.mne.bem module🔗

class meegpype.interfaces.mne.bem.MakeWatershedBEM(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)🔗

Bases: BaseInterface

Mandatory Inputs:

  • subject (a string) – Subject name (required).

  • subjects_dir (a pathlike object or string representing an existing directory) – Subjects directory.

Optional Inputs:

  • T1 (a boolean) – If True, pass the -T1 flag. By default (None), this takes the same value as gcaatlas.

  • atlas (a boolean) – Specify the –atlas option for mri_watershed.

  • brainmask (a string or os.PathLike object) – The filename for the brainmask output file, Can be for example ‘../../mri/brainmask.mgz’ to overwrite the brainmask obtained via recon-all -autorecon1.

  • copy (a boolean) – If True (default), use copies instead of symlinks for surfaces (if they do not already exist).

  • gcaatlas (a boolean) – Specify the –brain_atlas option for mri_watershed.

  • overwrite (a boolean) – Overwrite existing files.

  • preflood (a float) – Change the preflood height.

  • verbose (a boolean) – Enable verbose mode (printing of log messages).

  • volume (a string) – Defaults to T1.

Outputs:

  • brain_surf (a string or os.PathLike object referring to an existing file)

  • head (a string or os.PathLike object referring to an existing file)

  • inner_skull (a string or os.PathLike object referring to an existing file)

  • outer_skin (a string or os.PathLike object referring to an existing file)

  • outer_skull (a string or os.PathLike object referring to an existing file)

  • subject (a string) – Subject name.

  • subjects_dir (a pathlike object or string representing a directory) – Subjects directory.

  • watershed_brain_surf (a string or os.PathLike object referring to an existing file) – Original watershed brain surface.

  • watershed_inner_skull (a string or os.PathLike object referring to an existing file) – Original watershed inner skull surface.

  • watershed_outer_skin (a string or os.PathLike object referring to an existing file) – Original watershed outer skin surface.

  • watershed_outer_skull (a string or os.PathLike object referring to an existing file) – Original watershed outer skull surface.

class meegpype.interfaces.mne.bem.SetupForwardModel(from_file=None, resource_monitor=None, ignore_exception=False, **inputs)🔗

Bases: BaseInterface

Mandatory Inputs:

  • fname (a string or os.PathLike object) – Output base name. Will be prepend by -bem.fif and -sol.fif.

  • inner_skull (a pathlike object or string representing an existing file) – Inner skull surface (FreeSurfer format).

  • subject (a string) – Subject name (required).

Optional Inputs:

  • conductivity (an array) – Defines the brain compartment conductivity. The default value is 0.3 S/m.

  • ico (an integer) – The surface ico downsampling to use, e.g. 5=20484, 4=5120, 3=1280. If None, no subsampling is applied.

  • outer_skin (a pathlike object or string representing an existing file) – Outer skin surface (FreeSurfer format). Required for a 3-layer model.

  • outer_skull (a pathlike object or string representing an existing file) – Outer skull surface (FreeSurfer format). Required for a 3-layer model.

  • overwrite (a boolean) – Overwrite existing files.

  • verbose (a boolean) – Enable verbose mode (printing of log messages).

Outputs:

  • bem_solution (a pathlike object or string representing an existing file) – The resulting file containing the BEM solution.

  • bem_surfaces (a pathlike object or string representing an existing file) – The resulting file containing the BEM model.