Source reconstruction

• Source space region clustering
  • run()
  • _read_freesurfer_annotation()
  • _get_sphere_faces()
  • _get_mri_to_model_trans()
• Boundary element model (BEM)
  • BEM_mdl()
  • run()
  • _find_non_diag_omega()
  • _find_diag_omega()
• Coregistration, MEG to MRI
  • Coreg()
  • run()
  • plot_coregistration()
  • load_meg_ref_pts()
  • _calc_coreg()
  • _load_mri_ref_pts()
  • _format_fiducials()
  • _load_hd_surf()
  • _registrate_3d_points_restricted()
  • _get_ref_ptn_cnt()
  • _refine_registration()
  • _rm_bad_head_shape_pts()
  • _registrate_3d_points_free()
  • _translation()
  • _rotation()
  • _scaling()
  • _get_transformation_matrix()
  • _get_rot_and_scale_mat()
  • _get_trans_and_rot_mat()
  • _get_rot_mat()
• Cortical model
  • Cort_mdl()
  • get()
  • _read()
  • _create_source_mesh_model()
  • _match_source_mesh_model()
  • _rm_out_of_in_skull_vert()
  • _update_invalid_vertices()
• Freesurfer methods
  • init_fs_paths()
  • extract_mri_anatomy()
  • copy_fsavg_anatomy()
  • extract_skull_skin()
  • _create_fiducials()
  • _format_fiducials()
• Forward model
  • compute()
  • restrict()
  • _get_meg_coil_info()
  • _get_meg_coil_positions()
  • _comp_src_sen_contrib()
  • _calc_magnetic_fields()
  • _add_current_distribution()
  • _calc_bem_fields()
  • _calc_acc_hem_normals()
  • _find_vertex_clusters()
• Inverse model
  • Inv_mdl()
  • compute()
  • apply()
  • _calc_whitener()
  • _get_meg_channel_type_idx()
• Sensor covariance
  • Sen_cov()
  • run()
  • load()
  • _get_bio_channel_type_idx()
  • _empirically_estimate_cov()
  • _calc_sensor_noise_cov()
• Skull and skin models
  • Skull_skin_mdls()
  • read()
  • plot()
  • _load_and_orient_t1()
  • _plot_subplots()
• Sphere models
  • calculate_sphere_from_octahedron()
  • calculate_sphere_from_icosahedron()
  • read_sphere_from_icosahedron_in_fs_order()
  • prune_closeby_vert()
  • _tessellate_sphere()
• Subject to fs-avg
  • prepare()
  • compute()
  • apply()
  • _calc_small_to_default_vertices_proj()
  • _calc_mri_maps()
• Utility functions
  • run_subprocess_in_custom_working_directory()
  • fast_cross_product()
  • norm_vert()
  • magn_of_vec()
  • apply_inv_transformation()
  • calc_quat_angle()
  • orient_mat_to_block_format()
  • get_eigenbasis()
  • find_nearest_neighbor()
  • find_valid_vertices()