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Up to TkSurferGuide

Back to [:.../TkSurferIntroToScripting: TkSurferScripting]

Continue to [:TkSurferGuide/TkSurferReference: TkSurferReference]

Scripting

TableOfContents

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 vrmlsurf. mode is 0 for pts, 1 for gray, and 2 for curv.

Anchor(write_binary_dipoles) write_binary_dipoles

Desc. Will read the file name from dip.

Anchor(write_binary_decimation) write_binary_decimation

Desc. Will read the file name from dec.

Anchor(write_dipoles) write_dipoles

Desc. Will read the file name from dip.

Anchor(write_decimation) write_decimation

Desc. Will read the file name from dec.

Anchor(write_curv_images) write_curv_images

Desc. Will read the file name from targcurvim.

Anchor(write_fill_images) write_fill_images

Desc.

Anchor(fill_second_surface) fill_second_surface

Desc.

Anchor(subsample_dist) subsample_dist spacing

Desc. spacing is an integer.

Anchor(subsample_orient) subsample_orient spacing

Desc. spacing is an integer.

Anchor(write_subsample) write_subsample

Desc. Will read the file name from fs.

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 mode

Desc. This will swap a set field vertex rip fields, and then rip the surface. If mode is 1, will swap the oripflag and ripflag fields. If mode is 2, will set the oripflag field from the ripflag field and the ripflag field from the origripflag field. After the rip, all vertices will be unmarked.

Anchor(dilate_ripped) dilate_ripped

Desc.

Anchor(twocond) twocond condition condition

Desc. Both conditions are integers.

Anchor(cut_line) cut_line closed

Desc. closed should be 0 for an open line, and 1 for a closed line.

Anchor(plot_curv) plot_curv closed

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. closed should be 0 for an open curve, and 1 for a closed curve. The file is called surfer_curv.dat.

Anchor(draw_fundus) draw_fundus

Desc.

Anchor(plot_marked) plot_marked fileName

Desc. Generates a summary file of data from all marked vertices in fileName.

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 fileName

Desc. Reads an x/y vector from fileName and draws it to the screen.

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 degrees

Desc. `rotate_brain_y degrees Anchor(rotate_brain_z) rotate_brain_z degrees

Desc. degrees is a floating point number.

Anchor(translate_brain_x) translate_brain_x distance

Desc. `translate_brain_y distance Anchor(translate_brain_z) translate_brain_z distance

Desc. distance is in millimeter.

Anchor(scale_brain) scale_brain amount

Desc. amount is a floating point number.

Anchor(resize_window) resize_window size

Desc. size is an integer. The new window size will be sqaure with size x sizedimensions.

Anchor(move_window) move_window x y

Desc. x and y are integers.

Anchor(do_lighting_model) do_lighting_model light0 light1 light2 light3 offset

Desc. light0 through light3 are light levels from different positions and offset is overal ambient light. All values are floating points from 01.

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 subjtmpdir.

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 rightLeftFactor anteriorPosteriorFactor superiorInferiorFactor

Desc. All factors are floating point numbers.

Anchor(really_rotate_brain_x) really_rotate_brain_x degrees

Desc. `really_rotate_brain_y degrees Anchor(really_rotate_brain_z) really_rotate_brain_z degrees

Desc. Rotates the brain on the lh/rh axis. degrees is a floating point number.

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 dec.

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. tmid is the midpoint, dt is the delta to go on either side, and condition is the condition to use.

Anchor(load_var_from_sol) load_var_from_sol condition

Desc.

Anchor(compute_timecourses) compute_timecourses

Desc.

Anchor(filter_recs) filter_recs

Desc.

Anchor(read_rec) read_rec fileName

Desc.

Anchor(read_iop) read_iop fileName dipoleFileNumber

Desc.

Anchor(read_ncov) read_ncov fileName

Desc.

Anchor(normalize_time_courses) normalize_time_courses type

Desc. type should be 0 to set all values to 1, 1 for normalizing for baseline noise covariance, 2 for normalizing for white noise, 3 for normalizing by read noise covariance matrix, and 4 for unity gain.

Anchor(compute_timecourses) compute_timecourses

Desc.

Anchor(compute_pval_fwd) compute_pval_fwd pvalThreshold

Desc. pvalThreshold is a floating point number.

Anchor(compute_select_fwd) compute_select_fwd maximumDistance

Desc. maximumDistance is a floating point number in millimeters.

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 x y z

Desc. x y and z are floating point talairach values.

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 origcoords.

Anchor(read_canon_vertex_coordinates) read_canon_vertex_coordinates fileName

Desc.

Anchor(send_spherical_point) send_spherical_point subjectName canonicalFileName origFileName

Desc. subjectName is the subject for whom to write the cursor fiel. canonicalFileName is the file from which to read the canonical vetex positions. origFileName is the file from which to read the original vetex positions. Those filenames are relative to the subjectName. This will write to the edit.dat cursor file.

Anchor(send_to_subject) send_to_subject subjectName

Desc. Calls send_spherical_point with standard file names for canonicalFileName and origFileName.

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 vertexNumber

Desc. Inverts the vertex normal at the numbered vertex.

Anchor(invert_face) invert_face faceNumber

Desc. Inverts the face normal at the numbered face.

Anchor(mark_annotation) mark_annotation vertexNumber

Desc. Will mark all vertices with the same annotation value as the annotation value at the specified vertex.

Anchor(mark_faces) mark_faces vertexNumber

Desc. Marks all vertices in the face to which the specified vertex belongs.

Anchor(mark_face) mark_face faceNumber

Desc. Mark the specified face.

Anchor(dump_vertex) dump_vertex vertexNumber

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 surfaceFileName threshold

Desc. Reads vertex positions from surfaceFileName. For every vertex normal with a component longer than threshold, will set the overlay value at that vertex to the value of that component, otherwise sets the value to 0. threshold is a floating point number.

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 fileName

Desc.

Anchor(read_imag_vals) read_imag_vals fileName

Desc. Reads imaginary values from fileName.

Anchor(sol_plot) sol_plot timePoint plotType

Desc. Uses the dlat value in computing the range.

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 overlayField

Desc. Creates a new overlay layer with the values in the current label in overlay field overlayField.

Anchor(t_to_p) t_to_p DOF

Desc.

Anchor(f_to_p) f_to_p DOFnumerator DOFdenominator

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 fileName

Desc.

Anchor(read_and_smooth_parcellation) read_and_smooth_parcellation parcellationFileName colorTableFileName soapBubbleIterations modeFilterIterations

Desc. Reads a parcellation from parcellationFileName using colorTableFileName and performs soap bubble and mode filter on the values.

Anchor(read_parcellation) read_parcellation parcellationFileName colorTableFileName

Desc.

Anchor(deconvolve_weights) deconvolve_weights weightFileName scaleFileName

Desc.

Anchor(read_disc) read_disc subjectName

Desc.

Anchor(mask_label) mask_label labelFileName

Desc.

Anchor(orient_sphere) orient_sphere

Desc.

Anchor(dump_faces) dump_faces vertexNumber

Desc. Prints information about all faces connected to the specified vertex.

Anchor(load_gcsa) load_gcsa fileName

Desc.

Anchor(left_click) left_click x y

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 fileName

Desc.

Anchor(read_vertex_list) read_vertex_list fileName

Desc.

Anchor(draw_cursor) draw_cursor vertexNumber on

Desc. Draws the specified vertex in blue if on, or in the background color if not on.

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 vertexNumber

Desc.

Anchor(swap_vertex_fields) swap_vertex_fields field field

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 fileName field

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 fileName field

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 field

Desc. Reads the file name val.

Anchor(sclv_load_label_value_file) sclv_load_label_value_file fileName field

Desc.

Anchor(sclv_smooth) sclv_smooth numberOfSteps field

Desc.

Anchor(sclv_set_overlay_alpha) sclv_set_overlay_alpha alpha

Desc.

Anchor(sclv_set_current_field) sclv_set_current_field field

Desc.

Anchor(sclv_set_current_timepoint) sclv_set_current_timepoint timePoint condition

Desc.

Anchor(sclv_copy_view_settings_from_current_field) sclv_copy_view_settings_from_current_field toField fromField

Desc.

Anchor(sclv_copy_all_view_settings_from_current_field) sclv_copy_all_view_settings_from_current_field toField

Desc.

Anchor(sclv_copy_view_settings_from_field) sclv_copy_view_settings_from_field toField

Desc.

Anchor(sclv_set_current_threshold_from_percentile) sclv_set_current_threshold_from_percentile threshold midPoint slope

Desc.

Anchor(sclv_set_current_threshold_using_fdr) sclv_set_current_threshold_using_fdr rate markedOnly

Desc.

Anchor(sclv_send_histogram) sclv_send_histogram field

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 value

Desc.

Anchor(read_surface_vertex_set) read_surface_vertex_set field vertexSet

Desc.

Anchor(set_current_vertex_set) set_current_vertex_set

Desc.

Anchor(func_load_timecourse) func_load_timecourse fileName registrationType registrationFileName

Desc. registrationFileName is necessary only of registrationType is file.

Anchor(func_load_timecourse_offset) func_load_timecourse_offset fileName registrationType registrationFileName

Desc. registrationFileName is necessary only of registrationType is file.

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 fileName

Desc.

Anchor(labl_load_color_table) labl_load_color_table fileName

Desc.

Anchor(labl_load) labl_load fileName

Desc.

Anchor(labl_save) labl_save label fileName

Desc.

Anchor(labl_save_all) labl_save_all prefix

Desc.

Anchor(labl_import_annotation) labl_import_annotation fileName

Desc.

Anchor(labl_export_annotation) labl_export_annotation fileName

Desc.

Anchor(labl_new_from_marked_vertices) labl_new_from_marked_vertices

Desc.

Anchor(labl_mark_vertices) labl_mark_vertices index

Desc.

Anchor(labl_select) labl_select index

Desc.

Anchor(labl_set_name_from_table) labl_set_name_from_table index

Desc.

Anchor(labl_set_info) labl_set_info index name structureIndex visibility

Desc.

Anchor(labl_set_color) labl_set_color index red green blue

Desc.

Anchor(labl_remove) labl_remove index

Desc.

Anchor(labl_remove_all) labl_remove_all

Desc.

Anchor(labl_erode) labl_erode index

Desc.

Anchor(labl_dilate) labl_dilate index

Desc.

Anchor(labl_select_label_by_vno) labl_select_label_by_vno vertexNumber

Desc.

Anchor(labl_print_list) labl_print_list

Desc.

Anchor(labl_print_table) labl_print_table

Desc.

Anchor(path_select) path_select index

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 dontCrossPath dontCrossLabel dontFillUnlabeled dontCrossCuravature dontCrossThreshold multipleSeeds action argument

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 fileName

Desc.

Anchor(flip_normals) flip_normals axes

Desc. axes is a string containing x, y, or z, or any combination.

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.

TkSurferGuide/TkSurferScripting/TkSurferScriptingReference (last edited 2010-04-26 18:50:48 by KrishSubramaniam)