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Scripting
This section assumes you are familiar with Tcl and how to write basic scripts.
Most of TkSurfer's functions have Tcl bindings. As you have probably noticed, the interface is just a Tk/Tix window. You can look at the interface script, tksurfer.tcl, to see how most of the functionality is used. Following is a list of Tcl commands defined by TkSurfer. You can use these commands in your own scripts and call them with the -tcl command line option to execute them on startup. TkSurfer can run in a kind of batch mode in this fashion, although it still requires X and has to be able to open its main window.
You can also enter these script commands from the shell that TkSurfer was launched in. You can use the Tcl source command to load a script file from the Tcl shell as well.
This list is provided for reference. If you can figure out something that works, great, but it is not officially a feature of TkSurfer.
Commands
Functions arguments are listed by their name followed by their arguments. Arguments in square brackets are optional.
Anchor(swap_buffers) swap_buffers
Desc.
Anchor(to_single_buffer) to_single_buffer
Desc.
Anchor(to_double_buffer) to_double_buffer
Desc.
Anchor(open_window) open_window
Desc.
Anchor(help) help
Desc.
Anchor(redraw) redraw
Desc.
Anchor(redraw_second) redraw_second
Desc.
Anchor(shrink) shrink numberOfSteps
Desc.
Anchor(area_shrink) area_shrink numberOfSteps
Desc.
Anchor(sphere_shrink) sphere_shrink numberOfSteps radius
Desc. radius is in millimeters.
Anchor(ellipsoid_project) ellipsoid_project rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
Desc. All distances are in radius.
Anchor(ellipsoid_morph) ellipsoid_morph numberOfSteps rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance
Desc. All distances are in radius.
Anchor(ellipsoid_shrink) ellipsoid_shrink numberOfSteps radius
Desc. radius is in millimeters.
Anchor(ellipsoid_shrink_bug) ellipsoid_shrink_bug numberOfSteps radius length
Desc. radius and length is in millimeters.
Anchor(curv_shrink_to_fill) curv_shrink_to_fill numberOfSteps
Desc.
Anchor(smooth_curvim) smooth_curvim numberOfSteps
Desc.
Anchor(smooth_curv) smooth_curv numberOfSteps
Desc.
Anchor(smooth_val) smooth_val numberOfSteps
Desc.
Anchor(smooth_val_sparse) smooth_val_sparse numberOfSteps
Desc.
Anchor(smooth_curvim_sparse) smooth_curvim_sparse numberOfSteps
Desc.
Anchor(smooth_fs) smooth_fs numberOfSteps
Desc.
Anchor(add_subject_to_average_curvim) add_subject_to_average_curvim subjectName morphSubjectDirectory
Desc.
Anchor(read_curv_images) read_curv_images
Desc.
Anchor(read_stds) read_stds conditionNumber
Desc.
Anchor(read_second_binary_surf) read_second_binary_surf
Desc. Reads the file name from targsurf.
Anchor(read_second_binary_curv) read_second_binary_curv
Desc. Reads the file name from targcurv.
Anchor(normalize_second_binary_curv) normalize_second_binary_curv
Desc.
Anchor(curv_to_curvim) curv_to_curvim
Desc.
Anchor(second_surface_curv_to_curvim) second_surface_curv_to_curvim
Desc.
Anchor(curvim_to_second_surface) curvim_to_second_surface
Desc.
Anchor(swap_curv) swap_curv
Desc.
Anchor(curvim_to_surface) curvim_to_surface
Desc.
Anchor(read_binary_surf) read_binary_surf
Desc. Reads the file name from insurf.
Anchor(read_surf) read_surf fileName
Desc.
Anchor(save_surf) save_surf
Desc.
Anchor(restore_surf) restore_surf
Desc.
Anchor(show_surf) show_surf vertexSet
Desc. vertexSet is white, pial, or inflate.
Anchor(read_binary_curv) read_binary_curv
Desc. Reads the file name from curv.
Anchor(read_binary_sulc) read_binary_sulc
Desc. Reads the file name from sulc.
Anchor(read_binary_values) read_binary_values
Desc. Will read the value file from val.
Anchor(read_binary_values_frame) read_binary_values_frame
Desc. Will read the value file from val.
Anchor(read_annotated_image) read_annotated_image
Desc. Will read the file from annot.
Anchor(read_annotations) read_annotations fileName
Desc. fileName is an annotation file name, usually ending in .annot.
Anchor(read_binary_patch) read_binary_patch
Desc. Will read the file name from patch.
Anchor(read_fieldsign) read_fieldsign
Desc. Will read the file name from fs.
Anchor(read_fsmask) read_fsmask
Desc. Will read the file name from fm.
Anchor(write_binary_areas) write_binary_areas
Desc. Will read the file name from area.
Anchor(write_binary_surface) write_binary_surface
Desc. Will read the file name from outsurf.
Anchor(write_binary_curv) write_binary_curv
Desc. Will read the file name from curv.
Anchor(write_binary_sulc) write_binary_sulc
Desc. Will read the file name from sulc.
Anchor(write_binary_values) write_binary_values
Desc. Will read the file name from val.
Anchor(write_binary_patch) write_binary_patch
Desc. Will read the file name from patch.
Anchor(write_labeled_vertices) write_labeled_vertices
Desc. Will read the file name from label.
Anchor(read_labeled_vertices) read_labeled_vertices
Desc. Will read the file name from label.
Anchor(read_and_color_labeled_vertices) read_and_color_labeled_vertices red green blue
Desc. The colors are integers from 0-254.
Anchor(write_fieldsign) write_fieldsign
Desc. Will read the file name from fs.
Anchor(write_fsmask) write_fsmask
Desc. Will read the file name from fm.
Anchor(write_vrml) write_vrml mode Desc. Will read the file name from Anchor(write_binary_dipoles) write_binary_dipoles Desc. Will read the file name from Anchor(write_binary_decimation) write_binary_decimation Desc. Will read the file name from Anchor(write_dipoles) write_dipoles Desc. Will read the file name from Anchor(write_decimation) write_decimation Desc. Will read the file name from Anchor(write_curv_images) write_curv_images Desc. Will read the file name from Anchor(write_fill_images) write_fill_images Desc. Anchor(fill_second_surface) fill_second_surface Desc. Anchor(subsample_dist) subsample_dist Desc. Anchor(subsample_orient) subsample_orient Desc. Anchor(write_subsample) write_subsample Desc. Will read the file name from Anchor(compute_curvature) compute_curvature Desc. Anchor(compute_CMF) compute_CMF Desc. Anchor(compute_cortical_thickness) compute_cortical_thickness Desc. Anchor(clear_curvature) clear_curvature Desc. Anchor(clear_ripflags) clear_ripflags Desc. Anchor(restore_ripflags) restore_ripflags Desc. This will swap a set field vertex rip fields, and then rip the surface. If Anchor(dilate_ripped) dilate_ripped Desc. Anchor(twocond) twocond Desc. Both conditions are integers. Anchor(cut_line) cut_line Desc. Anchor(plot_curv) plot_curv Desc. Draws a curve between marked vertices, and generates a summary file of all vertices on that curve, including values of all the overlay layers and the distance form the first point. Anchor(draw_fundus) draw_fundus Desc. Anchor(plot_marked) plot_marked Desc. Generates a summary file of data from all marked vertices in Anchor(put_retinotopy_stats_in_vals) put_retinotopy_stats_in_vals Desc. Calculates retinotopy values at each vertex and stores them in the first overlay layer. Anchor(draw_vector) draw_vector Desc. Reads an x/y vector from Anchor(cut_plane) cut_plane Desc. Cuts a plane based on four marked vertices: three to define the plane, and one to indicate which area to not cut. Anchor(flatten) flatten Desc. Reads the file name from subjtmpdir. Anchor(normalize_binary_curv) normalize_binary_curv Desc. Anchor(normalize_area) normalize_area Desc. Anchor(shift_values) shift_values Desc. Anchor(swap_values) swap_values Desc. Anchor(swap_stat_val) swap_stat_val Desc. Anchor(swap_val_val2) swap_val_val2 Desc. Anchor(compute_angles) compute_angles Desc. Anchor(compute_fieldsign) compute_fieldsign Desc. Anchor(draw_radius) draw_radius Desc. Anchor(draw_theta) draw_theta Desc. Anchor(save_rgb) save_rgb Desc. Reads the file name from rgb. Anchor(save_rgb_cmp_frame) save_rgb_cmp_frame Desc. Reads the file name from rgb. Write an rgb frame file to be composed into a movie later. Anchor(rotate_brain_x) rotate_brain_x Desc. `rotate_brain_y Desc. Anchor(translate_brain_x) translate_brain_x Desc. `translate_brain_y Desc. Anchor(scale_brain) scale_brain Desc. Anchor(resize_window) resize_window Desc. Anchor(move_window) move_window Desc. Anchor(do_lighting_model) do_lighting_model Desc. Anchor(restore_zero_position) restore_zero_position Desc. Anchor(restore_initial_position) restore_initial_position Desc. Anchor(make_lateral_view) make_lateral_view Desc. Anchor(make_lateral_view_second) make_lateral_view_second Desc. Anchor(read_view_matrix) read_view_matrix Desc. Reads the file name from
Anchor(write_view_matrix) write_view_matrix
Desc. Reads the file name from subjtmpdir.
Anchor(read_really_matrix) read_really_matrix
Desc. Reads the file name from subjtmpdir.
Anchor(write_really_matrix) write_really_matrix
Desc. Reads the file name from subjtmpdir.
Anchor(really_translate_brain) really_translate_brain rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance Desc. All distances are in millimeters and can be floating point. Anchor(really_scale_brain) really_scale_brain Desc. All factors are floating point numbers. Anchor(really_rotate_brain_x) really_rotate_brain_x Desc. `really_rotate_brain_y Desc. Rotates the brain on the lh/rh axis. Anchor(align_sphere) align_sphere Desc. Anchor(really_center_brain) really_center_brain Desc. Anchor(really_center_second_brain) really_center_second_brain Desc. Anchor(really_align_brain) really_align_brain Desc. Anchor(read_binary_decimation) read_binary_decimation Desc. Reads the file name from
Anchor(read_binary_dipoles) read_binary_dipoles
Desc. Reads the file name from dip.
Anchor(load_vals_from_sol) load_vals_from_sol tmid dt condition Desc. Anchor(load_var_from_sol) load_var_from_sol Desc. Anchor(compute_timecourses) compute_timecourses Desc. Anchor(filter_recs) filter_recs Desc. Anchor(read_rec) read_rec Desc. Anchor(read_iop) read_iop Desc. Anchor(read_ncov) read_ncov Desc. Anchor(normalize_time_courses) normalize_time_courses Desc. Anchor(compute_timecourses) compute_timecourses Desc. Anchor(compute_pval_fwd) compute_pval_fwd Desc. Anchor(compute_select_fwd) compute_select_fwd Desc. Anchor(compute_pval_inv) compute_pval_inv Desc. Anchor(normalize_inverse) normalize_inverse Desc. Anchor(find_orig_vertex_coordinates) find_orig_vertex_coordinates Desc. Anchor(select_orig_vertex_coordinates) select_orig_vertex_coordinates Desc. Anchor(select_talairach_point) select_talairach_point Desc. Anchor(read_white_vertex_coordinates) read_white_vertex_coordinates Desc. Anchor(read_pial_vertex_coordinates) read_pial_vertex_coordinates Desc. Anchor(read_orig_vertex_coordinates) read_orig_vertex_coordinates Desc. Reads the file name from
Anchor(read_canon_vertex_coordinates) read_canon_vertex_coordinates fileName Desc. Anchor(send_spherical_point) send_spherical_point Desc. Anchor(send_to_subject) send_to_subject Desc. Calls send_spherical_point with standard file names for
Anchor(resend_to_subject) resend_to_subject
Desc. Calls send_to_subject with the sam subject name used in the previous send_to_subject call. Anchor(invert_surface) invert_surface Desc. Inverts the vertex normals for all unripped vertices in the surface, but not the faces. Anchor(fix_nonzero_vals) fix_nonzero_vals Desc. Sets the fixedval value for each vertex to 1 if the overlay value for that vertex is not 0, and to 0 if the value is 0. Anchor(invert_vertex) invert_vertex Desc. Inverts the vertex normal at the numbered vertex. Anchor(invert_face) invert_face Desc. Inverts the face normal at the numbered face. Anchor(mark_annotation) mark_annotation Desc. Will mark all vertices with the same annotation value as the annotation value at the specified vertex. Anchor(mark_faces) mark_faces Desc. Marks all vertices in the face to which the specified vertex belongs. Anchor(mark_face) mark_face Desc. Mark the specified face. Anchor(dump_vertex) dump_vertex Desc. Prints information about the specified vertex. Anchor(val_to_mark) val_to_mark Desc. Will mark all vertices with overlay values greater than the overlay threshold. Anchor(resize_brain) resize_brain Desc. Scales the brain according to the surface area to total area ration. Anchor(transform_brain) transform_brain Desc. Recenters the brain. Anchor(show_flat_regions) show_flat_regions Desc. Reads vertex positions from Anchor(val_to_stat) val_to_stat Desc. Copies the values of the overlay value field to the stat field. Anchor(stat_to_val) stat_to_val Desc. Copies the values of the stat field to the overlay value field. Anchor(read_soltimecourse) read_soltimecourse Desc. Anchor(read_imag_vals) read_imag_vals Desc. Reads imaginary values from
Anchor(sol_plot) sol_plot timePoint plotType Desc. Uses the Anchor(remove_triangle_links) remove_triangle_links Desc. Anchor(f_to_t) f_to_t Desc. Squares and takes the absolute value for every overlay value field in the vertices. Anchor(label_to_stat) label_to_stat Desc. Creates a new overlay layer with the values in the current label in overlay field
Anchor(t_to_p) t_to_p DOF Desc. Anchor(f_to_p) f_to_p Desc. Anchor(val_to_curv) val_to_curv Desc. Copies the first overlay values into the curvature values. Anchor(curv_to_val) curv_to_val Desc. Copies the curvature values into the first overlay values. Anchor(read_curv_to_val) read_curv_to_val Desc. Anchor(read_and_smooth_parcellation) read_and_smooth_parcellation Desc. Reads a parcellation from Anchor(read_parcellation) read_parcellation Desc. Anchor(deconvolve_weights) deconvolve_weights Desc. Anchor(read_disc) read_disc Desc. Anchor(mask_label) mask_label Desc. Anchor(orient_sphere) orient_sphere Desc. Anchor(dump_faces) dump_faces Desc. Prints information about all faces connected to the specified vertex. Anchor(load_gcsa) load_gcsa Desc. Anchor(left_click) left_click Desc. Simulates a click at the given window position. Anchor(plot_all_time_courses) plot_all_time_courses Desc. Anchor(read_plot_list) read_plot_list Desc. Anchor(read_vertex_list) read_vertex_list Desc. Anchor(draw_cursor) draw_cursor Desc. Draws the specified vertex in blue if
Anchor(mark_vertex) mark_vertex vertexNumber on Desc. Marks or unmarks a specified vertex. Anchor(draw_all_cursor) draw_all_cursor Desc. Anchor(draw_all_vertex_cursor) draw_all_vertex_cursor Desc. Anchor(clear_all_vertex_cursor) clear_all_vertex_cursor Desc. Anchor(send_current_labels) send_current_labels Desc. Anchor(select_vertex_by_vno) select_vertex_by_vno Desc. Anchor(swap_vertex_fields) swap_vertex_fields Desc. Anchor(clear_vertex_marks) clear_vertex_marks Desc. Anchor(clear_all_vertex_marks) clear_all_vertex_marks Desc. Anchor(close_marked_vertices) close_marked_vertices Desc. Anchor(undo_last_action) undo_last_action Desc. Anchor(sclv_read_from_dotw) sclv_read_from_dotw Desc. Anchor(sclv_read_binary_values) sclv_read_binary_values Desc. Anchor(sclv_read_from_dotw_frame) sclv_read_from_dotw_frame Desc. Anchor(sclv_read_binary_values_frame) sclv_read_binary_values_frame Desc. Anchor(sclv_read_from_volume) sclv_read_from_volume Desc. Anchor(sclv_read_bfile_values) sclv_read_bfile_values Desc. Anchor(sclv_write_dotw) sclv_write_dotw Desc. Reads the file name
Anchor(sclv_load_label_value_file) sclv_load_label_value_file fileName field Desc. Anchor(sclv_smooth) sclv_smooth Desc. Anchor(sclv_set_overlay_alpha) sclv_set_overlay_alpha Desc. Anchor(sclv_set_current_field) sclv_set_current_field Desc. Anchor(sclv_set_current_timepoint) sclv_set_current_timepoint Desc. Anchor(sclv_copy_view_settings_from_current_field) sclv_copy_view_settings_from_current_field Desc. Anchor(sclv_copy_all_view_settings_from_current_field) sclv_copy_all_view_settings_from_current_field Desc. Anchor(sclv_copy_view_settings_from_field) sclv_copy_view_settings_from_field Desc. Anchor(sclv_set_current_threshold_from_percentile) sclv_set_current_threshold_from_percentile Desc. Anchor(sclv_set_current_threshold_using_fdr) sclv_set_current_threshold_using_fdr Desc. Anchor(sclv_send_histogram) sclv_send_histogram Desc. Anchor(sclv_send_current_field_info) sclv_send_current_field_info Desc. Anchor(sclv_get_normalized_color_for_value) sclv_get_normalized_color_for_value Desc. Anchor(read_surface_vertex_set) read_surface_vertex_set Desc. Anchor(set_current_vertex_set) set_current_vertex_set Desc. Anchor(func_load_timecourse) func_load_timecourse Desc. Anchor(func_load_timecourse_offset) func_load_timecourse_offset Desc. Anchor(func_select_marked_vertices) func_select_marked_vertices Desc. Anchor(func_select_label) func_select_label Desc. Anchor(func_clear_selection) func_clear_selection Desc. Anchor(func_graph_timecourse_selection) func_graph_timecourse_selection Desc. Anchor(func_print_timecourse_selection) func_print_timecourse_selection Desc. Anchor(labl_load_color_table) labl_load_color_table Desc. Anchor(labl_load) labl_load Desc. Anchor(labl_save) labl_save Desc. Anchor(labl_save_all) labl_save_all Desc. Anchor(labl_import_annotation) labl_import_annotation Desc. Anchor(labl_export_annotation) labl_export_annotation Desc. Anchor(labl_new_from_marked_vertices) labl_new_from_marked_vertices Desc. Anchor(labl_mark_vertices) labl_mark_vertices Desc. Anchor(labl_select) labl_select Desc. Anchor(labl_set_name_from_table) labl_set_name_from_table Desc. Anchor(labl_set_info) labl_set_info Desc. Anchor(labl_set_color) labl_set_color Desc. Anchor(labl_remove) labl_remove Desc. Anchor(labl_remove_all) labl_remove_all Desc. Anchor(labl_erode) labl_erode Desc. Anchor(labl_dilate) labl_dilate Desc. Anchor(labl_select_label_by_vno) labl_select_label_by_vno Desc. Anchor(labl_print_list) labl_print_list Desc. Anchor(labl_print_table) labl_print_table Desc. Anchor(path_select) path_select Desc. Anchor(path_new_path_from_marked_vertices) path_new_path_from_marked_vertices Desc. Anchor(path_remove_selected_path) path_remove_selected_path Desc. Anchor(fill_flood_from_cursor) fill_flood_from_cursor Desc. Anchor(draw_curvature_line) draw_curvature_line Desc. Anchor(get_marked_vnos) get_marked_vnos Desc. Anchor(get_selected_path_vnos) get_selected_path_vnos Desc. Anchor(save_tiff) save_tiff Desc. Anchor(flip_normals) flip_normals Desc. Anchor(mark_contiguous_vertices_over_thresh) mark_contiguous_vertices_over_thresh Desc. Anchor(mark_contiguous_vertices_with_similar_curvature) mark_contiguous_vertices_with_similar_curvature Desc. Anchor(rip_all_vertices_except_contiguous_upripped) rip_all_vertices_except_contiguous_upripped Desc.