osl_ephys.source_recon.rhino.forward_model#

Forward modelling in RHINO.

Functions#

forward_model(subjects_dir, subject[, model, ...])

Compute forward model.

make_fwd_solution(subjects_dir, subject, src, bem[, ...])

Calculate a forward solution for a subject. This is a RHINO wrapper for mne.make_forward_solution.

setup_volume_source_space(subjects_dir, subject[, ...])

Set up a volume source space grid inside the inner skull surface.

Module Contents#

osl_ephys.source_recon.rhino.forward_model.forward_model(subjects_dir, subject, model='Single Layer', gridstep=8, mindist=4.0, exclude=0.0, eeg=False, meg=True, verbose=False)[source]#

Compute forward model.

Parameters:

  • subjects_dir (string) – Directory to find RHINO subject dirs in.

  • subject (string) – Subject name dir to find RHINO files in.

  • model (string) – ‘Single Layer’ or ‘Triple Layer’ ‘Single Layer’ to use single layer (brain/cortex) ‘Triple Layer’ to three layers (scalp, inner skull, brain/cortex)

  • gridstep (int) – A grid will be constructed with the spacing given by gridstep in mm generating a volume source space.

  • mindist (float) – Exclude points closer than this distance (mm) to the bounding surface.

  • exclude (float) – Exclude points closer than this distance (mm) from the center of mass of the bounding surface.

  • eeg (bool) – Whether to compute forward model for eeg sensors

  • meg (bool) – Whether to compute forward model for meg sensors

osl_ephys.source_recon.rhino.forward_model.make_fwd_solution(subjects_dir, subject, src, bem, meg=True, eeg=True, mindist=0.0, ignore_ref=False, n_jobs=1, verbose=None)[source]#

Calculate a forward solution for a subject. This is a RHINO wrapper for mne.make_forward_solution.

See mne.make_forward_solution for the full set of parameters, with the exception of:

Parameters:

  • subjects_dir (string) – Directory to find RHINO subject dirs in.

  • subject (string) – Subject name dir to find RHINO files in.

Returns:

fwd – The forward solution.

Return type:

instance of Forward

Notes

Forward modelling is done in head space.

The coords of points to reconstruct to can be found in the output here:

>>> fwd['src'][0]['rr'][fwd['src'][0]['vertno']]

where they are in head space in metres.

The same coords of points to reconstruct to can be found in the input here:

>>> src[0]['rr'][src[0]['vertno']]

where they are in native MRI space in metres.

osl_ephys.source_recon.rhino.forward_model.setup_volume_source_space(subjects_dir, subject, gridstep=5, mindist=5.0, exclude=0.0)[source]#

Set up a volume source space grid inside the inner skull surface.

This is a RHINO specific version of mne.setup_volume_source_space.

Parameters:

  • subjects_dir (string) – Directory to find RHINO subject dirs in.

  • subject (string) – Subject name dir to find RHINO files in.

  • gridstep (int) – A grid will be constructed with the spacing given by gridstep in mm generating a volume source space.

  • mindist (float) – Exclude points closer than this distance (mm) to the bounding surface.

  • exclude (float) – Exclude points closer than this distance (mm) from the center of mass of the bounding surface.

Returns:

src – A single source space object.

Return type:

mne.SourceSpaces

See also

mne.setup_volume_source_space()

Notes

This is a RHINO specific version of mne.setup_volume_source_space, which can handle smri’s that are niftii files. This specifically uses the inner skull surface in:

>>> get_coreg_filenames(subjects_dir, subject)['bet_inskull_surf_file']

to define the source space grid.

This will also copy the:

>>> get_coreg_filenames(subjects_dir, subject)['bet_inskull_surf_file']

file to:

``subjects_dir/subject/bem/inner_skull.surf`

since this is where mne expects to find it when mne.make_bem_model is called.

The coords of points to reconstruct to can be found in the output here:

>>> src[0]['rr'][src[0]['vertno']]

where they are in native MRI space in metres.