Index

_

__init__() (simnibs.mesh_tools.mesh_io.ElementData method) (simnibs.mesh_tools.mesh_io.Elements method) (simnibs.mesh_tools.mesh_io.Msh method) (simnibs.mesh_tools.mesh_io.NodeData method) (simnibs.mesh_tools.mesh_io.Nodes method) (simnibs.utils.file_finder.SubjectFiles method)

A

atlases_surfaces (in module simnibs.utils.file_finder)

B

binary (simnibs.mesh_tools.mesh_io.Msh attribute)

C

calc_B() (in module simnibs.simulation.biot_savart) calc_fields() (in module simnibs.simulation.fem) cerebrum_mask (simnibs.utils.file_finder.SubjectFiles attribute)

charm_atlas_path (in module simnibs.utils.file_finder) charm_log (simnibs.utils.file_finder.SubjectFiles attribute) CircularArray (class in simnibs.optimization.tes_flex_optimization.electrode_layout) conf2mni_nonl (simnibs.utils.file_finder.SubjectFiles attribute)

E

eeg_cap_1010 (simnibs.utils.file_finder.SubjectFiles attribute) eeg_cap_folder (simnibs.utils.file_finder.SubjectFiles attribute) electric_dipole() (in module simnibs.simulation.fem) ElectrodeArrayPair (class in simnibs.optimization.tes_flex_optimization.electrode_layout) ElementData (class in simnibs.mesh_tools.mesh_io)

Elements (class in simnibs.mesh_tools.mesh_io) elm (simnibs.mesh_tools.mesh_io.Msh attribute) elm_number (simnibs.mesh_tools.mesh_io.ElementData attribute) (simnibs.mesh_tools.mesh_io.Elements attribute) elm_type (simnibs.mesh_tools.mesh_io.Elements attribute) elmdata (simnibs.mesh_tools.mesh_io.Msh attribute)

F

field_name (simnibs.mesh_tools.mesh_io.ElementData attribute) (simnibs.mesh_tools.mesh_io.NodeData attribute) final_labels (simnibs.utils.file_finder.SubjectFiles attribute) final_labels_MNI (simnibs.utils.file_finder.SubjectFiles attribute)

final_tissues_LUT (in module simnibs.utils.file_finder) fn (simnibs.mesh_tools.mesh_io.Msh attribute) fnamehead (simnibs.utils.file_finder.SubjectFiles attribute) freesurfer_templates (in module simnibs.utils.file_finder)

G

get_atlas() (in module simnibs.utils.file_finder)

H

head_mesh (simnibs.utils.file_finder.SubjectFiles attribute)

hemi_mask (simnibs.utils.file_finder.SubjectFiles attribute) hemispheres (simnibs.utils.file_finder.SubjectFiles attribute)

L

label_prep_folder (simnibs.utils.file_finder.SubjectFiles attribute)

labeling (simnibs.utils.file_finder.SubjectFiles attribute) labeling_LUT (in module simnibs.utils.file_finder)

M

mni2conf_12dof (simnibs.utils.file_finder.SubjectFiles attribute) mni2conf_6dof (simnibs.utils.file_finder.SubjectFiles attribute) mni2conf_nonl (simnibs.utils.file_finder.SubjectFiles attribute) mni2subject_coords() (in module simnibs.utils.transformations)

mni_transf_folder (simnibs.utils.file_finder.SubjectFiles attribute) mni_volume (in module simnibs.utils.file_finder) morph_data (simnibs.utils.file_finder.SubjectFiles attribute) Msh (class in simnibs.mesh_tools.mesh_io)

N

node_coord (simnibs.mesh_tools.mesh_io.Nodes attribute) node_number (simnibs.mesh_tools.mesh_io.NodeData attribute) node_number_list (simnibs.mesh_tools.mesh_io.Elements attribute) NodeData (class in simnibs.mesh_tools.mesh_io) nodedata (simnibs.mesh_tools.mesh_io.Msh attribute) Nodes (class in simnibs.mesh_tools.mesh_io) nodes (simnibs.mesh_tools.mesh_io.Msh attribute)

norm_image (simnibs.utils.file_finder.SubjectFiles attribute) nr (simnibs.mesh_tools.mesh_io.ElementData attribute) (simnibs.mesh_tools.mesh_io.Elements attribute) (simnibs.mesh_tools.mesh_io.NodeData attribute) (simnibs.mesh_tools.mesh_io.Nodes attribute) nr_comp (simnibs.mesh_tools.mesh_io.ElementData attribute) (simnibs.mesh_tools.mesh_io.NodeData attribute)

P

parahippo_mask (simnibs.utils.file_finder.SubjectFiles attribute)

R

read_curv() (in module simnibs.mesh_tools.mesh_io) read_freesurfer_surface() (in module simnibs.mesh_tools.mesh_io) read_gifti_surface() (in module simnibs.mesh_tools.mesh_io)

read_msh() (in module simnibs.mesh_tools.mesh_io) read_stl() (in module simnibs.mesh_tools.mesh_io) reference_volume (simnibs.utils.file_finder.SubjectFiles attribute) RegionOfInterest (class in simnibs.utils.region_of_interest)

S

segmentation_folder (simnibs.utils.file_finder.SubjectFiles attribute) simnibs_logo (in module simnibs.utils.file_finder) subcortical_mask (simnibs.utils.file_finder.SubjectFiles attribute) subid (simnibs.utils.file_finder.SubjectFiles attribute) subject2mni_coords() (in module simnibs.utils.transformations)

subject_atlas() (in module simnibs.utils.transformations) SubjectFiles (class in simnibs.utils.file_finder) subpath (simnibs.utils.file_finder.SubjectFiles attribute) summary_report (simnibs.utils.file_finder.SubjectFiles attribute) surface_folder (simnibs.utils.file_finder.SubjectFiles attribute) surfaces (simnibs.utils.file_finder.SubjectFiles attribute)

T

T1 (simnibs.utils.file_finder.SubjectFiles attribute) T1_bias_corrected (simnibs.utils.file_finder.SubjectFiles attribute) T1_denoised (simnibs.utils.file_finder.SubjectFiles attribute) T1_upsampled (simnibs.utils.file_finder.SubjectFiles attribute) T2_reg (simnibs.utils.file_finder.SubjectFiles attribute) T2_reg_bias_corrected (simnibs.utils.file_finder.SubjectFiles attribute) T2_reg_denoised (simnibs.utils.file_finder.SubjectFiles attribute) T2_upsampled (simnibs.utils.file_finder.SubjectFiles attribute) tag1 (simnibs.mesh_tools.mesh_io.Elements attribute) tag2 (simnibs.mesh_tools.mesh_io.Elements attribute) tcd_json_schema (in module simnibs.utils.file_finder)

tdcs() (in module simnibs.simulation.fem) tdcs_leadfield() (in module simnibs.simulation.fem) tdcs_neumann() (in module simnibs.simulation.fem) template_coregistered (simnibs.utils.file_finder.SubjectFiles attribute) templates (in module simnibs.utils.file_finder) tensor_file (simnibs.utils.file_finder.SubjectFiles attribute) TesFlexOptimization (class in simnibs.opt_struct) tissue_labeling_upsampled (simnibs.utils.file_finder.SubjectFiles attribute) tms_coil() (in module simnibs.simulation.fem) tms_dadt() (in module simnibs.simulation.fem) tms_many_simulations() (in module simnibs.simulation.fem) TmsFlexOptimization (class in simnibs.opt_struct)

V

value (simnibs.mesh_tools.mesh_io.ElementData attribute) (simnibs.mesh_tools.mesh_io.NodeData attribute)

W

write_curv() (in module simnibs.mesh_tools.mesh_io) write_freesurfer_surface() (in module simnibs.mesh_tools.mesh_io)

write_geo_spheres() (in module simnibs.mesh_tools.mesh_io) write_geo_text() (in module simnibs.mesh_tools.mesh_io) write_msh() (in module simnibs.mesh_tools.mesh_io)