Cortical model

This module may be employed to read and cortical models.

src_rec.cort_mdl.Cort_mdl(lh_vert, lh_faces, lh_valid_vert, rh_vert, rh_faces, rh_valid_vert, octa_mdl_vert, octa_mdl_faces)

Container populated with the following cortical surface (MRI) based items.

Parameters:

• lh_vert (np.ndarray, shape(lh_vtx_cnt, 3)) – White matter surface model vertices (left hemisphere).

• lh_faces (np.ndarray, shape(lh_face_cnt, 3)) – White matter surface model faces (left hemisphere).

• lh_valid_vert (np.ndarray, shape(rh_vtx_cnt,)) – Valid flags for white matter surface model vertices (left hemisphere).

• rh_vert (np.ndarray, shape(rh_vtx_cnt, 3)) – White matter surface model vertices (right hemisphere).

• rh_faces (np.ndarray, shape(rh_face_cnt, 3)) – White matter surface model faces (right hemisphere).

• lh_valid_vert – Valid flags for white matter surface model vertices (right hemisphere).

• octa_model_vert (np.ndarray, shape(octa_mdl_vtx_cnt, 3)) – Octamodel vertices (left hemisphere).

• octa_model_faces (np.ndarray, shape(octa_mdl_face_cnt, 3)) – Octamodel faces (right hemisphere).

src_rec.cort_mdl.get(anatomy_path, subj_name, signal_type, coreg, bem_mdl)

Read and filter cortical freesurfer data.

Parameters:

• anatomy_path (string) – Path to the anatomy folder. This folder should contain a sub-folder for each subject, to be pupulated with the corresponding structural data.

• subj_name (string) – Name of the subject.

• signal_type (string) – Mode is either “EEG” or “MEG”.

• coreg (finnpy.src_rec.coregistration_meg_mri.Coreg) – Container with different transformation matrices

• bem_mdl (finnpy.src_rec.bem_mdl.BEM_mdl) –

  Container class, populed with the following items:

  vertlist() of np.ndarray, [shape(scaled_vtx_cnt, 3), …]

  Remaining vertices of a skin/skull model vertices.

  faceslist() of np.ndarray, [shape(scaled_face_cnt, 3), …]

  Remaining faces of a skin/skull model faces.

  faces_normalnp.ndarray, shape(scaled_face_cnt, 3)

  Normals of the individual remaining inner skull faces.

  faces_areanp.ndarray, shape(scaled_face_cnt)

  Surface area of the remaining faces.

  bem_solutionnp.ndarray, shape(scaled_vtx_cnt, scaled_vtx_cnt)

  BEM solution (preliminary step for the calculation of the forward model).

Returns:

cort_mdl – Container populated with the following items:

• lh_vertnp.ndarray, shape(lh_vtx_cnt, 3)

  White matter surface model vertices (left hemisphere).

• lh_facesnp.ndarray, shape(lh_face_cnt, 3)

  White matter surface model faces (left hemisphere).

• lh_valid_vertnp.ndarray, shape(lh_vtx_cnt,)

  Valid flags for white matter surface model vertices (left hemisphere).

• rh_vertnp.ndarray, shape(rh_vtx_cnt, 3)

  White matter surface model vertices (right hemisphere).

• rh_facesnp.ndarray, shape(rh_face_cnt, 3)

  White matter surface model faces (right hemisphere).

• rh_valid_vertnp.ndarray, shape(rh_vtx_cnt,)

  Valid flags for white matter surface model vertices (right hemisphere).

• octa_model_vertnp.ndarray, shape(octa_mdl_vtx_cnt, 3)

  Octamodel vertices (left hemisphere).

• octa_model_facesnp.ndarray, shape(octa_mdl_face_cnt, 3)

  Octamodel faces (right hemisphere).

Return type:

finnpy.src_rec.cort_mdl.Cort_mdl

src_rec.cort_mdl._read(anatomy_path, subj_name, signal_type, coreg)

Read cortical freesurfer data.

Parameters:

• anatomy_path (string) – Path to the anatomy folder. This folder should contain a sub-folder for each subject, to be pupulated with the corresponding structural data.

• subj_name (string) – Name of the subject.

• signal_type (string) – Either “EEG” or “MEG”.

• coreg (finnpy.src_rec.coregistration_meg_mri.Coreg) – Container with different transformation matrices

Returns:

result –

• lh_white_vertnp.ndarray, shape(lh_white_vtx_cnt, 3)

  White matter surface model vertices (left hemisphere).

• lh_white_facesnp.ndarray, shape(lh_white_face_cnt, 3)

  White matter surface model faces (left hemisphere).

• rh_white_vertnp.ndarray, shape(rh_white_vtx_cnt, 3)

  White matter surface model vertices (right hemisphere).

• rh_white_facesnp.ndarray, shape(rh_white_face_cnt, 3)

  White matter surface model faces (right hemisphere).

• lh_sphere_vertnp.ndarray, shape(lh_sphere_vtx_cnt, 3)

  Spherical freesurfer head model vertices (left hemisphere).

• rh_sphere_vertnp.ndarray, shape(rh_sphere_vtx_cnt, 3)

  Spherical freesurfer head model vertices (right hemisphere).

Return type:

tuple of (np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray, np.ndarray)

src_rec.cort_mdl._update_invalid_vertices(approx_surface, white_vert, valid_vert)

Update invalid vertices.

Parameters:

• approx_surface (scipy.spatial._qhull.Delaunay) – Approximate in/out skull/skin surface.

• white_vert (np.ndarray, shape(white_vtx_cnt, 3)) – White matter surface vertices.

• valid_vert (np.ndarray, shape(white_vtx_cnt, 3)) – Binary list of valid vertices.

Returns:

trans_white_vert – Transformed vertices.

Return type:

np.ndarray, shape(white_vtx_cnt, 3)