talairach.c File Reference

#include <volume_io/internal_volume_io.h>
#include <bicpl/vols.h>

Include dependency graph for talairach.c:

Go to the source code of this file.

Defines
#define	TALAIRACH_OFFSET   16.0
#define	FALSE   0
#define	TRUE   1
Functions
private void	read_talairach_coordinate_system (void)
private void	check_initialized (void)
public void	convert_voxel_to_talairach (Real x_voxel, Real y_voxel, Real z_voxel, int nx_voxels, int ny_voxels, int nz_voxels, Real *x_tal, Real *y_tal, Real *z_tal)
public void	convert_talairach_to_voxel (Real x_tal, Real y_tal, Real z_tal, int nx_voxels, int ny_voxels, int nz_voxels, Real *x_voxel, Real *y_voxel, Real *z_voxel)
private Real	convert_to_mm (Real tal, int n_planes, Real limit_low, Real limit_high, Real brain_dist_low, Real brain_dist_high, Real brain_limit_low, Real brain_limit_high)
public void	convert_talairach_to_mm (Real x_tal, Real y_tal, Real z_tal, Real *x_mm, Real *y_mm, Real *z_mm)
private Real	convert_from_mm (Real mm, int n_planes, Real limit_low, Real limit_high, Real brain_dist_low, Real brain_dist_high, Real brain_limit_low, Real brain_limit_high)
public void	convert_mm_to_talairach (Real x_mm, Real y_mm, Real z_mm, Real *x_tal, Real *y_tal, Real *z_tal)
Variables
private int	nx = 128
private int	ny = 128
private int	nz = 80
private Real	x_low = -1.28
private Real	x_high = 1.28
private Real	y_low = -1.28
private Real	y_high = 1.28
private Real	z_low = -0.50
private Real	z_high = 1.10
private Real	x_dist_minus_1 = -67.0
private Real	x_dist_1 = 67.0
private Real	y_dist_minus_1 = -86.0
private Real	y_dist_1 = 86.0
private Real	z_dist_0 = 0.0
private Real	z_dist_1 = 75.0
private BOOLEAN	initialized = FALSE

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Define Documentation

#define FALSE   0

Definition at line 24 of file talairach.c. Referenced by average_polygon_normals(), check_correct_deformation_lines(), check_correct_deformation_polygons(), check_correct_general_lines(), check_correct_general_polygons(), check_correct_parametric_polygons(), check_correct_subsampled_polygons(), check_initialize_colours(), check_install_bintree_delete_function(), check_range(), check_voxel_for_boundary(), check_voxel_for_isovalue(), clip_line_to_box(), clip_polygon_against_box(), colour_code_points(), compute_polygon_normals(), compute_polygons_model_info(), compute_quadmesh_normals(), compute_statistics(), contains_value(), create_box_filtered_volume(), create_case(), create_cropped_volume(), create_edge_for_face(), create_label_volume(), create_label_volume_from_file(), create_polygon_neighbours(), create_polygon_point_neighbours(), create_tetrahedral_sphere(), create_tube(), cube_is_small_enough(), define_colour_coding_user_defined(), deformation_model_includes_average(), dilate_voxels_3d(), do_more_resampling(), does_voxel_contain_value_range(), fast_approx_sqrt(), fill_connected_voxels(), find_axial_plane(), find_boundary_in_direction(), find_neighbour_face(), find_path_between_polygons(), find_polygon_with_vertex(), find_volume_crop_bounds(), find_voxel_edge_index(), free_colours(), get_3D_neighbour_directions(), get_8bit_rgb_pixel_lookup(), get_average_curvature(), get_bitlist_bit_3d(), get_cross_section(), get_filter_slices(), get_input_volume_label_limits(), get_int_argument(), get_interpolation_weights_2d(), get_lines_arc_point(), get_max_point_cube_distance(), get_next_object_traverse(), get_object_colour(), get_plane_segment_intersection(), get_planes(), get_polygon_vertex_curvatures(), get_polygons_around_vertex(), get_prediction_weights_3d(), get_prefix_argument(), get_quadmesh_point(), get_range_of_object(), get_range_of_polynomial(), get_real_argument(), get_smooth_surface_curvature(), get_string_argument(), get_tessellation_of_polygons_sphere(), get_two_d_coordinate(), get_two_point_prediction(), get_volume_voxel_activity(), get_voxel_case_struct(), gradient_steps_minimize_function(), half_sample_sphere_tessellation(), initialize_deformation_model(), initialize_deformation_parameters(), initialize_quadmesh(), input_globals_file(), input_object_type(), input_original_positions(), input_texture_values_binary(), input_volume_header_only(), insert_neighbours(), int_voxel_is_within_volume(), interpolate_volume_to_slice(), intersect_lines_2d(), intersect_ray_polygon(), intersect_ray_polygon_points(), intersect_ray_triangle(), intersect_ray_with_cube(), io_polygons(), is_clear_slab(), is_point_inside_surface(), is_single_closed_curve(), line_intersects_ellipsoid(), line_segment_intersects_plane(), load_label_volume(), lookup_colour(), lookup_colour_name(), lookup_in_hash2_table(), lookup_in_hash_table(), minimize_along_line(), modify_labels_in_range(), node_tightly_bounds_object(), objects_are_same_topology(), optimize_simplex(), output_texture_values_binary(), output_volume_free_format(), perform_amoeba(), point_within_polygon_2d(), point_within_triangle_2d(), ray_intersects_sphere(), ray_intersects_tube(), read_talairach_coordinate_system(), recursive_intersect_ray(), remove_from_hash2_table(), remove_from_hash_table(), resample_volume(), reverse_object_normals(), rotmat_to_ang(), save_label_volume(), scan_object_to_volume(), set_colour_coding_over_colour(), set_colour_coding_type(), set_global_variable(), set_label_volume_real_range(), set_up_to_search_ray(), should_change_this_one(), singular_value_decomposition(), smooth_points(), smooth_resample_volume(), split_node(), strings_equivalent(), subdivide_bintree(), subdivide_polygons(), volumes_are_same_grid(), voxel_contains_range(), voxel_is_within_volume(), and voxel_might_contain_boundary().

#define TALAIRACH_OFFSET   16.0

Definition at line 22 of file talairach.c. Referenced by convert_mm_to_talairach(), and convert_talairach_to_mm().

#define TRUE   1

Definition at line 25 of file talairach.c. Referenced by check_correct_deformation_lines(), check_correct_deformation_polygons(), check_correct_general_lines(), check_correct_general_polygons(), check_correct_model_lines(), check_correct_model_polygons(), check_correct_subsampled_polygons(), check_initialize_colours(), check_initialized(), check_install_bintree_delete_function(), check_range(), check_voxel_for_boundary(), check_voxel_for_isovalue(), clip_line_to_box(), clip_polygon_against_box(), compute_polygons_model_info(), compute_statistics(), contains_value(), create_case(), create_cropped_volume(), create_label_volume_from_file(), create_object(), create_polygons_visibilities(), create_tube(), cube_is_small_enough(), define_colour_coding_user_defined(), deformation_model_includes_average(), dilate_voxels_3d(), does_voxel_contain_value_range(), fast_approx_sqrt(), fill_connected_voxels(), find_axial_plane(), find_boundary_in_direction(), find_neighbour_face(), find_path_between_polygons(), find_polygon_with_vertex(), find_volume_crop_bounds(), find_voxel_edge_index(), flatten_around_vertex_to_sphere(), follow_edge(), free_colours(), get_3D_neighbour_directions(), get_8bit_rgb_pixel_lookup(), get_average_curvature(), get_cross_section(), get_filter_slices(), get_input_volume_label_limits(), get_int_argument(), get_interpolation_weights_2d(), get_lines_arc_point(), get_max_point_cube_distance(), get_next_object_traverse(), get_object_colour(), get_plane_segment_intersection(), get_planes(), get_polygon_vertex_curvatures(), get_polygons_around_vertex(), get_prediction_weights_2d(), get_prediction_weights_3d(), get_prefix_argument(), get_quadmesh_point(), get_range_of_object(), get_real_argument(), get_smooth_surface_curvature(), get_string_argument(), get_two_d_coordinate(), get_two_point_prediction(), get_volume_voxel_activity(), gradient_steps_minimize_function(), initialize_colour_coding(), input_object_type(), input_original_positions(), input_texture_values_binary(), input_volume_header_only(), insert_neighbours(), int_voxel_is_within_volume(), intersect_lines_2d(), intersect_ray_tube_segment(), io_polygons(), is_clear_slab(), is_point_inside_surface(), is_single_closed_curve(), line_intersects_ellipsoid(), line_segment_intersects_plane(), load_label_volume(), lookup_colour(), lookup_colour_name(), lookup_in_hash2_table(), lookup_in_hash_table(), minimize_along_line(), modify_labels_in_range(), node_tightly_bounds_object(), objects_are_same_topology(), optimize_simplex(), perform_amoeba(), perturb_line_points(), point_within_polygon_2d(), read_talairach_coordinate_system(), recursive_intersect_ray(), remove_from_hash2_table(), remove_from_hash_table(), rotmat_to_ang(), save_label_volume(), set_global_variable(), set_random_seed(), set_up_to_search_ray(), set_use_compressed_polygons_flag(), should_change_this_one(), singular_value_decomposition(), smooth_lines(), smooth_points(), split_node(), strings_equivalent(), subdivide_polygons(), use_compressed_polygons(), volumes_are_same_grid(), voxel_contains_range(), voxel_is_within_volume(), and voxel_might_contain_boundary().

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Function Documentation

private void check_initialized (  void   )

Definition at line 63 of file talairach.c. References initialized, read_talairach_coordinate_system(), and TRUE.

private Real convert_from_mm (  Real  mm, int  n_planes, Real  limit_low, Real  limit_high, Real  brain_dist_low, Real  brain_dist_high, Real  brain_limit_low, Real  brain_limit_high )

Definition at line 360 of file talairach.c. Referenced by convert_mm_to_talairach().

public void convert_mm_to_talairach (  Real  x_mm, Real  y_mm, Real  z_mm, Real *  x_tal, Real *  y_tal, Real *  z_tal )

Definition at line 397 of file talairach.c. References check_initialized(), convert_from_mm(), nx, ny, nz, TALAIRACH_OFFSET, x_dist_1, x_dist_minus_1, x_high, x_low, y_dist_1, y_dist_minus_1, y_high, y_low, z_dist_0, z_dist_1, z_high, and z_low.

public void convert_talairach_to_mm (  Real  x_tal, Real  y_tal, Real  z_tal, Real *  x_mm, Real *  y_mm, Real *  z_mm )

Definition at line 320 of file talairach.c. References check_initialized(), convert_to_mm(), nx, ny, nz, TALAIRACH_OFFSET, x_dist_1, x_dist_minus_1, x_high, x_low, y_dist_1, y_dist_minus_1, y_high, y_low, z_dist_0, z_dist_1, z_high, and z_low.

public void convert_talairach_to_voxel (  Real  x_tal, Real  y_tal, Real  z_tal, int  nx_voxels, int  ny_voxels, int  nz_voxels, Real *  x_voxel, Real *  y_voxel, Real *  z_voxel )

Definition at line 244 of file talairach.c. References check_initialized(), nx, ny, and nz. Referenced by io_tag_point().

private Real convert_to_mm (  Real  tal, int  n_planes, Real  limit_low, Real  limit_high, Real  brain_dist_low, Real  brain_dist_high, Real  brain_limit_low, Real  brain_limit_high )

Definition at line 282 of file talairach.c. Referenced by convert_talairach_to_mm().

public void convert_voxel_to_talairach (  Real  x_voxel, Real  y_voxel, Real  z_voxel, int  nx_voxels, int  ny_voxels, int  nz_voxels, Real *  x_tal, Real *  y_tal, Real *  z_tal )

Definition at line 206 of file talairach.c. References check_initialized(), nx, ny, and nz. Referenced by io_tag_point().

private void read_talairach_coordinate_system (  void   )

Definition at line 86 of file talairach.c. References FALSE, nx, ny, nz, TRUE, x_dist_1, x_dist_minus_1, x_high, x_low, y_dist_1, y_dist_minus_1, y_high, y_low, z_dist_0, z_dist_1, z_high, and z_low. Referenced by check_initialized().

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Variable Documentation

private BOOLEAN initialized = FALSE

Definition at line 45 of file talairach.c.

private int nx = 128

Definition at line 27 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), convert_talairach_to_voxel(), convert_voxel_to_talairach(), create_bitlist_3d(), find_polygon_normal(), find_polygon_normal_no_normalize(), get_bitlist_3d_sizes(), intersect_ray_triangle(), point_within_polygon_2d(), and read_talairach_coordinate_system().

private int ny = 128

Definition at line 28 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), convert_talairach_to_voxel(), convert_voxel_to_talairach(), create_bitlist_3d(), find_polygon_normal(), find_polygon_normal_no_normalize(), get_bitlist_3d_sizes(), intersect_ray_triangle(), point_within_polygon_2d(), and read_talairach_coordinate_system().

private int nz = 80

Definition at line 29 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), convert_talairach_to_voxel(), convert_voxel_to_talairach(), create_bitlist_3d(), find_polygon_normal(), find_polygon_normal_no_normalize(), get_bitlist_3d_sizes(), intersect_ray_triangle(), point_within_polygon_2d(), and read_talairach_coordinate_system().

private Real x_dist_1 = 67.0

Definition at line 39 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real x_dist_minus_1 = -67.0

Definition at line 38 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real x_high = 1.28

Definition at line 32 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real x_low = -1.28

Definition at line 31 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real y_dist_1 = 86.0

Definition at line 41 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real y_dist_minus_1 = -86.0

Definition at line 40 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real y_high = 1.28

Definition at line 34 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real y_low = -1.28

Definition at line 33 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real z_dist_0 = 0.0

Definition at line 42 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real z_dist_1 = 75.0

Definition at line 43 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real z_high = 1.10

Definition at line 36 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

private Real z_low = -0.50

Definition at line 35 of file talairach.c. Referenced by convert_mm_to_talairach(), convert_talairach_to_mm(), and read_talairach_coordinate_system().

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