Index

A

add_curv_stats() (brainload.braindescriptors.BrainDescriptors method) add_custom_measure_stats() (brainload.braindescriptors.BrainDescriptors method) add_parcellation_stats() (brainload.braindescriptors.BrainDescriptors method) add_segmentation_stats() (brainload.braindescriptors.BrainDescriptors method) add_single_segmentation_stats() (brainload.braindescriptors.BrainDescriptors method)

add_standard_stats() (brainload.braindescriptors.BrainDescriptors method) annot() (in module brainload) (in module brainload.annotations) AnnotQuery (class in brainload.annotations) apply_affine() (in module brainload.spatial) apply_affine_3D() (in module brainload.spatial)

B

BrainDescriptors (class in brainload.braindescriptors) brainload module brainload.annotations module brainload.braindescriptors module brainload.brainlocate module brainload.brainvoxlocate module brainload.brainwrite module

brainload.freesurferdata module brainload.meshexport module brainload.nitools module brainload.spatial module brainload.stats module BrainLocate (class in brainload.brainlocate) BrainVoxLocate (class in brainload.brainvoxlocate)

C

check_for_curv_stats_files() (brainload.braindescriptors.BrainDescriptors method) check_for_custom_measure_stats_files() (brainload.braindescriptors.BrainDescriptors method) check_for_hemi_dependent_file() (brainload.braindescriptors.BrainDescriptors method) check_for_hemi_independent_file() (brainload.braindescriptors.BrainDescriptors method) check_for_NaNs() (brainload.braindescriptors.BrainDescriptors method)

check_for_parcellation_stats_files() (brainload.braindescriptors.BrainDescriptors method) check_for_segmentation_stats_files() (brainload.braindescriptors.BrainDescriptors method) color_rgbt_to_rgba() (in module brainload.annotations) compute_labels() (brainload.annotations.AnnotQuery method) coords_a2s() (in module brainload.spatial) coords_s2a() (in module brainload.spatial)

D

deg2rad() (in module brainload.spatial) detect_subjects_in_directory() (in module brainload) (in module brainload.nitools)

do_subject_files_exist() (in module brainload.nitools)

E

export_mesh_nocolor_to_file() (in module brainload) extract_column_from_table_data() (in module brainload.stats)

extract_field_from_table_data() (in module brainload.stats) extract_table_data_indices_where() (in module brainload.stats)

F

fill_template_filename() (in module brainload.nitools)

fsaverage_mesh() (in module brainload) (in module brainload.freesurferdata)

G

get_affine_matrix_MNI152_to_MNI305() (in module brainload.spatial) get_affine_matrix_MNI305_to_MNI152() (in module brainload.spatial) get_atlas_region_names() (in module brainload.annotations) get_atlas_region_names_hardcoded() (in module brainload.annotations) get_closest_not_unknown() (brainload.brainvoxlocate.BrainVoxLocate method) get_closest_vertex() (brainload.brainlocate.BrainLocate method) get_closest_vertex_and_distance() (brainload.brainlocate.BrainLocate method) get_equivalent_voxel_of_raw_volume_in_conformed_volume() (in module brainload.spatial) get_freesurfer_matrix_ras2vox() (in module brainload.spatial) get_freesurfer_matrix_vox2ras() (in module brainload.spatial) get_morphometry_file_path() (in module brainload.freesurferdata) get_n_neighborhood_indices_3D() (in module brainload.spatial) get_n_neighborhood_indices_3D_points() (in module brainload.spatial) get_n_neighborhood_start_stop_indices_3D() (in module brainload.spatial) get_n_neighborhood_start_stop_indices_3D_points() (in module brainload.spatial) get_num_fsaverage_verts_per_hemi() (in module brainload.freesurferdata) get_ras_coords_at_voxel_crs() (brainload.brainvoxlocate.BrainVoxLocate method) get_standard_space_morphometry_file_path() (in module brainload.freesurferdata) get_stats_table_column_names() (in module brainload.stats)

get_surface_file_path() (in module brainload.freesurferdata) get_surface_vertices_overlay_text_file_lines() (in module brainload.brainwrite) get_surface_vertices_overlay_volume_data() (in module brainload.brainwrite) get_surface_vertices_overlay_volume_data_1color() (in module brainload.brainwrite) get_vertex_label_colors() (brainload.annotations.AnnotQuery method) get_vertex_label_names() (brainload.annotations.AnnotQuery method) get_volume_data_with_custom_marks() (in module brainload.brainwrite) get_vox2ras_and_ras2vox_from_nifti_file() (in module brainload.freesurferdata) get_voxel_crs_at_ras_coords() (brainload.brainvoxlocate.BrainVoxLocate method) get_voxel_segmentation_labels() (brainload.brainvoxlocate.BrainVoxLocate method) group() (in module brainload) (in module brainload.freesurferdata) group_native() (in module brainload) (in module brainload.freesurferdata) group_stats() (in module brainload.stats) group_stats_aparc() (in module brainload.stats) group_stats_aparc_a2009s() (in module brainload.stats) group_stats_aparc_DKTatlas() (in module brainload.stats) group_stats_aseg() (in module brainload.stats) group_stats_by_row() (in module brainload.stats)

H

hemi_range() (in module brainload) (in module brainload.freesurferdata)

L

label() (in module brainload) (in module brainload.annotations) label_to_mask() (in module brainload.annotations)

load_subject_mesh_files() (in module brainload.freesurferdata) load_subject_morphometry_data_files() (in module brainload.freesurferdata) load_vertex_indices() (in module brainload.nitools) load_voxel_indices() (in module brainload.nitools)

M

mask_data_using_label() (in module brainload.annotations) measures_to_numpy() (in module brainload.stats) merge_morphometry_data() (in module brainload.freesurferdata) mesh_to_obj() (in module brainload) (in module brainload.meshexport) mesh_to_off() (in module brainload.meshexport) mesh_to_ply() (in module brainload) (in module brainload.meshexport) mirror_3D_coordinates_at_axis() (in module brainload.spatial) module brainload brainload.annotations brainload.braindescriptors brainload.brainlocate brainload.brainvoxlocate brainload.brainwrite brainload.freesurferdata brainload.meshexport brainload.nitools brainload.spatial brainload.stats

P

parse_curve_stats() (in module brainload.stats) parse_curve_stats_file() (in module brainload.stats)

parse_registration_matrix() (in module brainload.spatial) parse_talairach_file() (in module brainload.freesurferdata) point_mirror_3D_coordinates() (in module brainload.spatial)

R

rad2deg() (in module brainload.spatial) read_annotation_md() (in module brainload.annotations) read_BIDS_participants_file() (in module brainload.nitools) read_fs_morphometry_data_file_and_record_meta_data() (in module brainload.freesurferdata) read_fs_surface_file_and_record_meta_data() (in module brainload.freesurferdata) read_label_md() (in module brainload.annotations) read_lookup_file() (in module brainload.freesurferdata) read_m3z_file() (in module brainload.freesurferdata) read_mgh_file() (in module brainload.freesurferdata) read_mgh_header_matrices() (in module brainload.freesurferdata) read_subjects_file() (in module brainload) (in module brainload.nitools)

read_vertex_list_file() (in module brainload.annotations) region_data_native() (in module brainload.annotations) region_stats() (in module brainload.annotations) register_dat_matrix() (in module brainload.stats) report_descriptors() (brainload.braindescriptors.BrainDescriptors method) rhi() (in module brainload) (in module brainload.freesurferdata) rhv() (in module brainload) (in module brainload.freesurferdata) rotate_3D_coordinates_around_axes() (in module brainload.spatial)

S

save() (brainload.braindescriptors.BrainDescriptors method) save_vertex_indices() (in module brainload.nitools) scalars_to_colors_clist() (in module brainload.meshexport) scalars_to_colors_matplotlib() (in module brainload.meshexport) scale_3D_coordinates() (in module brainload.spatial) stat() (in module brainload) (in module brainload.stats) stats_table_region_label_column_name() (in module brainload.stats) stats_table_to_numpy() (in module brainload.stats) stats_table_to_numpy_by_row() (in module brainload.stats)

subject() (in module brainload) (in module brainload.freesurferdata) subject_avg() (in module brainload) (in module brainload.freesurferdata) subject_data_native() (in module brainload) (in module brainload.freesurferdata) subject_data_standard() (in module brainload) (in module brainload.freesurferdata) subject_mesh() (in module brainload) (in module brainload.freesurferdata)

T

translate_3D_coordinates_along_axes() (in module brainload.spatial)

typelist_for_aparc_atlas_stats() (in module brainload.stats) typelist_for_aseg_stats() (in module brainload.stats)

V

vertices_to_label() (in module brainload.annotations)

W

write_BIDS_participants_file() (in module brainload.nitools) write_lines_to_text_file() (in module brainload.nitools)

write_subjects_file() (in module brainload.nitools) write_voldata_to_mgh_file() (in module brainload.brainwrite) write_voldata_to_nifti_file() (in module brainload.brainwrite)