• TkSurferGuide
• TkSurferScripting
• TkSurferScriptingReference

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.

Variables

These variables are used to turn on and off certain display characteristics. The way to set a flag is:

set gaLinkedVars(VARIABLENAME) VALUE
UpdateLinkedVarGroup GROUP

Here is a table listing the variables, valid values, group names, and functionality.

Commands

Functions arguments are listed by their name followed by their arguments. Arguments in square brackets are optional.

Anchor(align_sphere) align_sphere

• Given two marked points on the spherical surface, the first will specify the z-axis (the 1st pole of the sphere), and the second the x-axis (the orientation of the vertical meridian).

Anchor(clear_all_vertex_marks) clear_all_vertex_marks

• Unmarks all vertices (necessary if the array of marked vertices and the vertex fields' marked status gets out of sync, e.g. you set marked fields directly).

Anchor(clear_curvature) clear_curvature

• Sets all curvature values to 0.

Anchor(clear_ripflags) clear_ripflags

• Unrips all vertices.

Anchor(clear_vertex_marks) clear_vertex_marks

• Unmarks the marked vertices.

Anchor(close_marked_vertices) close_marked_vertices

• Adds the first marked vertex to the end of the list of marked vertices.

Anchor(compute_curvature) compute_curvature

• Computes the curvature based on vertex positions.

Anchor(curv_to_val) curv_to_val

• Copies the curvature values into the first overlay values.

Anchor(cut_line) cut_line closed

• Creates a line of ripped vertices on the surface between marked vertices in the order that they were marked. closed should be 0 for an open line, and 1 for a closed line.

Anchor(cut_plane) cut_plane

• Cuts a plane based on four marked vertices: three to define the plane, and one to indicate which area to not cut.

Anchor(dilate_ripped) dilate_ripped

• Dilates ripped areas, increasing their size by a vertex.

Anchor(do_lighting_model) do_lighting_model light0 light1 light2 light3 offset

• Changes the lighting setup for the scene. light0 through light3 are light levels from different positions and offset is overal ambient light. All values are floating points from 0-1.

Anchor(draw_cursor) draw_cursor vertexNumber on

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

Anchor(dump_vertex) dump_vertex vertexNumber

• Prints information about the specified vertex. vertexNumber is an integer.

Anchor(f_to_t) f_to_t

• Squares and takes the absolute value for every overlay value field in the vertices.

Anchor(find_orig_vertex_coordinates) find_orig_vertex_coordinates

• Performs the Save Cursor function. Writes the current cursor location to the edit.dat file.

Anchor(fix_nonzero_vals) fix_nonzero_vals

• 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(flip_normals) flip_normals axes

• Flips all the normal vectors at the vertices, changing the sign of the component values. axes is a string containing x, y, or z, or any combination, specifying which vector components to flip.

Anchor(func_clear_selection) func_clear_selection

• Clears the functional time course selection.

Anchor(func_graph_timecourse_selection) func_graph_timecourse_selection

• Plots the graph for the time course. If more than one vertices are selected by the time course, will plot the average of the values.

Anchor(func_load_timecourse) func_load_timecourse fileName registrationType registrationFileName

• Loads a time course from fileName. You must also specify a registrationType, which should be 0 to find a registration file in the same directory as the data, 1 to use an identity registration, and 2 to specify a file. If 2 is the registrationType, use registrationFileName to specify the file. The time course will be displayed in a new window.

registrationFileName is necessary only of registrationType is file.

Anchor(func_load_timecourse_offset) func_load_timecourse_offset fileName registrationType registrationFileName

• Loads a time course offset from fileName. You should already have a time course loaded. You must also specify a registrationType, which should be 0 to find a registration file in the same directory as the data, 1 to use an identity registration, and 2 to specify a file. If 2 is the registrationType, use registrationFileName to specify the file.

registrationFileName is necessary only of registrationType is file.

Anchor(func_print_timecourse_selection) func_print_timecourse_selection fileName

• Prints a text file summarizing the data selected in the functional time course.

Anchor(func_select_label) func_select_label

• Selects the vertices in the current label for the functional time course. Needs a call to func_graph_timecourse_selection to plot the graph.

Anchor(func_select_marked_vertices) func_select_marked_vertices

• Selects the marked vertices in the surface for the functional time course. Needs a call to func_graph_timecourse_selection to plot the graph.

Anchor(invert_face) invert_face faceNumber

• Inverts the face normal at the numbered face. faceNumber is an integer.

Anchor(fill_flood_from_cursor) fill_flood_from_cursor dontCrossPath dontCrossLabel dontFillUnlabeled dontCrossCuravature dontCrossThreshold multipleSeeds action argument

• Initiates a flood fill starting at the cursor. dontCrossPath should be 1 or 0, specifying whether the fill should cross paths. dontCrossLabel should be 1 or 0, specifying whether the fill should cross into labels or only stay in unlabeled vertices. dontFillUnlabeled should be 1 or 0 and specifies whether the fill should fill unlabeled vertices. dontCrossCurvature should be 1 or 0, specifying whether the fill should fill vertices that have a different curvature sign than the first vertex. dontCrossThreshold should be 1 or 0, specifying whether vertices with overlay values below the functional threshold should be field. multipleSeeds should be 1 or 0, specfifying whether or not to use all marked vertices as new seeds. action should be one of the following:

Anchor(get_marked_vnos) get_marked_vnos

• Returns a list of marked vertices.

Anchor(get_selected_path_vnos) get_selected_path_vnos

• Returns a list of vertices in the selected path.

Anchor(invert_surface) invert_surface

• Inverts the vertex normals for all unripped vertices in the surface, but not the faces.

Anchor(invert_vertex) invert_vertex vertexNumber

• Inverts the vertex normal at the numbered vertex. vertexNumber is an integer.

Anchor(label_to_stat) label_to_stat overlayField

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

Anchor(labl_dilate) labl_dilate label

• Expands a label by adding all vertices immediately adjacent to the label. label should be a valid label index.

Anchor(labl_erode) labl_erode label

• Shrinks a label by excluding all border vertices in the label. label should be a valid label index.

Anchor(labl_export_annotation) labl_export_annotation fileName

• Exports all labels marked as structures to an annotation.

Anchor(labl_import_annotation) labl_import_annotation fileName

• Important an annotation file as a series of label.

Anchor(labl_load) labl_load fileName

• Loads the label in fileName and adds it to the Labels window.

Anchor(labl_load_color_table) labl_load_color_table fileName

• Loads a color table for labels to use from fileName.

Anchor(labl_mark_vertices) labl_mark_vertices label

• Marks the vertices in a label. label should be a valid label index.

Anchor(labl_new_from_marked_vertices) labl_new_from_marked_vertices

• Creates a new label from the marked vertices.

Anchor(labl_print_list) labl_print_list

• Prints a list of label information to the shell

Anchor(labl_print_table) labl_print_table

• Prints the color table to the shell.

Anchor(labl_remove) labl_remove label

• Deletes a label. label should be a valid label index.

Anchor(labl_remove_all) labl_remove_all

• Deletes all labels.

Anchor(labl_save) labl_save label fileName

• Saves a label to fileName. label should be a valid label index.

Anchor(labl_save_all) labl_save_all prefix

• Saves all labels with a given prefix directory location.

Anchor(labl_select) labl_select label

• Marks the vertices in a label. label should be a valid label index.

Anchor(labl_select_label_by_vno) labl_select_label_by_vno vertexNumber

• Selects a label containing the given vertex number. If there are multiple labels occupying this vertex, successive calls to this function with the same vertex number will cycle through those labels. vertexNumber should be a valid vertex index.

Anchor(labl_set_color) labl_set_color label red green blue

• Sets the color for a label. label should be a valid label index. red, green, and blue should be integers from 0-255.

Anchor(labl_set_info) labl_set_info label name structureIndex visibility

• Sets information for a label. label should be a valid label index. name is a text string that will show up in the Label window and in the label display. structureIndex should be -1 if it's a free label or a valid index in the current lookup table if it's a structure label. visibility should be 1 or 0.

Anchor(labl_set_name_from_table) labl_set_name_from_table label

• Sets a label's name from its structure index from the lookup table. label should be a valid label index.

Anchor(left_click) left_click x y

• Simulates a click at the given window position. x and y should be integers.

Anchor(make_lateral_view) make_lateral_view

• Changes the view to show the surface laterally.

Anchor(mark_annotation) mark_annotation vertexNumber

• Will mark all vertices with the same annotation value as the annotation value at the specified vertex. vertexNumber is an integer.

Anchor(mark_contiguous_vertices_over_thresh) mark_contiguous_vertices_over_thresh

• Performs a flood fill from the cursor, marking all vertices that have overlay values above the threshold. (This is the Fill Stats tool.)

Anchor(mark_contiguous_vertices_with_similar_curvature) mark_contiguous_vertices_with_similar_curvature

• Performs a flood fill from the cursor, marking all vertices that have curvature values the same sign as the curvature at the seed. (This is the Fill Curvature tool.)

Anchor(mark_face) mark_face faceNumber

• Marks all vertices in the specified face. faceNumber is an integer.

Anchor(mark_faces) mark_faces vertexNumber

• Marks all vertices in the face to which the specified vertex belongs. vertexNumber is an integer.

Anchor(mark_vertex) mark_vertex vertexNumber on

• Marks or unmarks a specified vertex. vertexNumber is an integer, and on is 0 for off and 1 for on.

Anchor(mask_label) mask_label labelFileName

• This reads and marks a label file, and then for every vertex not marked, clears the overlay values.

Anchor(move_window) move_window x y

• Moves the window to a new location. x and y are integers and are global screen coordinates, with 0,0 in the top left corner of the screen.

Anchor(path_new_path_from_marked_vertices) path_new_path_from_marked_vertices

• Creates a new path using the marked vertices. Connects the marked vertices in the order they were marked to create the path.

Anchor(path_remove_selected_path) path_remove_selected_path

• Deletes the selected path.

Anchor(path_select) path_select path

• Selects the specified path. path should be a valid path index.

Anchor(plot_curv) plot_curv closed

• 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(read_annotations) read_annotations fileName

• Deprecated, replaced by labl_import_annotation. fileName is an annotation file name, usually ending in .annot.

Anchor(read_binary_curv) read_binary_curv

• Loads a curvature file into the surface. Reads the file name from curv.

Anchor(read_binary_decimation) read_binary_decimation

• Reads decimation values onto the surface from a file. Reads the file name from dec.

Anchor(read_binary_dipoles) read_binary_dipoles

• Reads dipole balues onto the surface from a file. Reads the file name from dip.

Anchor(read_binary_patch) read_binary_patch

• Reads a patch file into the surface. Will read the file name from patch.

Anchor(read_binary_sulc) read_binary_sulc

• Reads a sulcus file into the curvature display. Reads the file name from sulc.

Anchor(read_binary_surf) read_binary_surf

• Loads the main surface from a surface file. Reads the file name from insurf.

Anchor(read_binary_values) read_binary_values

• Deprecated, replaced by sclv_read_from_dotw. Will read the value file from val.

Anchor(read_binary_values_frame) read_binary_values_frame

• Deprecated, replaced by sclv_read_from_dotw_frame. Will read the value file from val.

Anchor(read_canon_vertex_coordinates) read_canon_vertex_coordinates fileName

• Reads the vertex coordinates from a file into the canonical vertex set.

Anchor(read_curv_to_val) read_curv_to_val fileName

• Reads a curvature file into the first overlay layer.

Anchor(read_fieldsign) read_fieldsign

• Reads field sign values from a file. Will read the file name from fs.

Anchor(read_fsmask) read_fsmask

• Reads the field sign mask from a file. Will read the file name from fm.

Anchor(read_imag_vals) read_imag_vals fileName

• Reads imaginary values from fileName.

Anchor(read_labeled_vertices) read_labeled_vertices

• Deprecated, replaced by labl_load. Will read the file name from label.

Anchor(read_orig_vertex_coordinates) read_orig_vertex_coordinates

• Reads the vertex coordinates from a file into the orig vertex set. Reads the file name from origcoords.

Anchor(read_pial_vertex_coordinates) read_pial_vertex_coordinates

• Reads the vertex coordinates from a file called ?h.pial where where ? is the current hemisphere into the pial vertex set.

Anchor(read_really_matrix) read_really_matrix

• Reads a matrix to transform the surface vertices. Reads the file name from subjtmpdir.

Anchor(read_surface_vertex_set) read_surface_vertex_set field fileName

• Reads a set of vertices from the fle in fileName. field should be one of the following:

Anchor(read_view_matrix) read_view_matrix

• Reads a view matrix from a file. Reads the file name from subjtmpdir.

Anchor(read_white_vertex_coordinates) read_white_vertex_coordinates

• Reads the vertex coordinates from a file called ?h.white where ? is the current hemisphere into the original vertex set.

Anchor(really_center_brain) really_center_brain

• Translates the surface coordinates to an average of all vertex coordinates.

Anchor(really_rotate_brain_x) really_rotate_brain_x degrees

• Rotates the surface vertices around the x axis. degrees is a floating point number.

Anchor(really_rotate_brain_y) really_rotate_brain_y degrees

• Rotates the surface vertices around the y axis. degrees is a floating point number.

Anchor(really_rotate_brain_z) really_rotate_brain_z degrees

• Rotates the surface vertices around the z axis. degrees is a floating point number.

Anchor(really_translate_brain) really_translate_brain rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance

• Translates the surface vertices along the specified axes. All distances are in millimeters and can be floating point.

Anchor(redraw) redraw

• Redraws the graphics window. It is necessary to call this after using other script commands to change the viewing state.

Anchor(resend_to_subject) resend_to_subject

• Calls send_to_subject with the sam subject name used in the previous send_to_subject call.

Anchor(resize_brain) resize_brain

• Scales the brain according to the surface area to total area ratio.

Anchor(resize_window) resize_window size

• Resizes the graphics window. size is an integer. The new window size will be sqaure with size x sizedimensions.

Anchor(restore_ripflags) restore_ripflags mode

• 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(restore_initial_position) restore_initial_position

• Restores the view to a medial view.

Anchor(restore_zero_position) restore_zero_position

• Restores the view to a medial view.

Anchor(rip_all_vertices_except_contiguous_upripped) rip_all_vertices_except_contiguous_upripped

• Performs a flood fill from the cursor, ripping all other vertices that are not contiguous to the seed point. (This is the Fill Uncut Area tool.)

Anchor(rotate_brain_x) rotate_brain_x degrees

• Rotates the view around the x axis. degrees should be a floating point number.

Anchor(rotate_brain_y) rotate_brain_y degrees

• Rotates the view around the y axis. degrees should be a floating point number.

Anchor(rotate_brain_z) rotate_brain_z degrees

• Rotates the view around the z axis. degrees should be a floating point number.

Anchor(save_rgb) save_rgb

• Saves the contents of the view to a file in RGB format. Reads the file name from rgb.

Anchor(save_rgb_cmp_frame) save_rgb_cmp_frame

• Reads the file name from rgb. Write an rgb frame file to be composed into a movie later.

Anchor(save_tiff) save_tiff fileName

• Saves the current graphics contents as a TIFF file.

Anchor(scale_brain) scale_brain zoomFactor

• Zooms the view. zoomFactor is a floating point number; values greater than 1 make the brain appear larger, and from 0 to 1, smaller.

Anchor(sclv_copy_all_view_settings_from_current_field) sclv_copy_all_view_settings_from_current_field

• Copies the settings from the current overlay to all other overlay layers.

Anchor(sclv_copy_view_settings_from_current_field) sclv_copy_view_settings_from_current_field field

• Copies the overlay settings from the current layer to another. field should be one of the field values in sclv_read_from_dotw.

Anchor(sclv_copy_view_settings_from_field) sclv_copy_view_settings_from_field tofield toField

• Copies the overlay settings from one layer to another. toField and fromField should be one of the field values in sclv_read_from_dotw.

Anchor(sclv_get_normalized_color_for_value) sclv_get_normalized_color_for_value value

• Converts an overlay value in the current field to an rgb color triple, returned as a list of floats. value should be a valid value in the current overlay layer.

Anchor(sclv_load_label_value_file) sclv_load_label_value_file fileName field

• Reads a label value file from fileName in an overlay field. field should be one of the field values in sclv_read_from_dotw. The label value file is a list of lines specifying a label name (such as an anatomical label from an LUT), a value, and a hemisphere.

Anchor(sclv_read_bfile_values) sclv_read_bfile_values

• Deprecated, replaced by sclv_read_from_volume.

Anchor(sclv_read_binary_values) sclv_read_binary_values

• Deprecated, replaced by sclv_read_from_dotw.

Anchor(sclv_read_binary_values_frame) sclv_read_binary_values_frame fileName field

• Deprecated, replaced by sclv_read_from_dotw_frame.

Anchor(sclv_read_from_dotw) sclv_read_from_dotw fileName field

• Reads an overlay layer from the file specified in dotw format. field should be one of the following:

Anchor(sclv_read_from_volume) sclv_read_from_volume field fileName registrationType [registrationFileName]

• Reads an overlay layer from a volume file. The volume can either be a full 3D volume of overlay data, or a volume encoded value file. For the former, a registration file must be provided. field must be an overlay field, see sclv_read_from_dotw for values. registrationType should be one of the following:

• If the registrationType is 0, then registrationFileName must be provided, otherwise it can be omitted.

Anchor(sclv_send_histogram) sclv_send_histogram field

• Tells tksurfer to resend the histogram information for a layer. Might be done after the overlay layer has changed, to force an update. field should be one of the field values in sclv_read_from_dotw.

Anchor(sclv_send_current_field_info) sclv_send_current_field_info

• Tells tksurfer to resend the overlay information for a layer. Might be done after the overlay layer has changed, to force an update. field should be one of the field values in sclv_read_from_dotw.

Anchor(sclv_set_current_field) sclv_set_current_field field

• Sets the current overlay field. field should be should be one of the field values in sclv_read_from_dotw.

Anchor(sclv_set_current_threshold_from_percentile) sclv_set_current_threshold_from_percentile min mid max

• Sets the current layer's threshold based on a percentile of values. min, mid, and max should be floating numbers from 0-100 representing percentages which will be mapped to overlay values to be used to set the threshold.

Anchor(sclv_set_current_threshold_using_fdr) sclv_set_current_threshold_using_fdr rate markedOnly

• Sets the current overlay's threshold using false discovery rate. rate is a floating point number representing the rate, and markedOnly should be 1 or 0 specifying whether to only calculate over marked vertices.

Anchor(sclv_set_current_timepoint) sclv_set_current_timepoint timePoint condition

• Sets the time point and condition for the current overlay field. timePoint and condition should be integer values in the range of the current overlay's number of time pooints and conditions.

Anchor(sclv_set_overlay_alpha) sclv_set_overlay_alpha alpha

• Sets the overlay alpha. This controls the translucency for overlay display. alpha should be from 0 - 1, with 1 being opaque.

Anchor(sclv_smooth) sclv_smooth numberOfSteps field

• Smooths an overlay layer. numberOfSteps is an integer. field should be one of the field values in sclv_read_from_dotw.

Anchor(sclv_write_dotw) sclv_write_dotw field

• Writes the given overlay field to a dotw file. Reads the file name val. field should be one of the field values in sclv_read_from_dotw.

Anchor(select_orig_vertex_coordinates) select_orig_vertex_coordinates

• Performs the Read Cursor function. Reads the cursor location from the edit.dat file.

Anchor(select_talairach_point) select_talairach_point x y z

• Takes the given talairach coordinate, writes it to the edit.dat file, and then sets the cursor to that point. x y and z are floating point talairach values.

Anchor(select_vertex_by_vno) select_vertex_by_vno vertexNumber

• Selects the given vertex as the cursor. vertexNumber is an integer.

Anchor(send_current_labels) send_current_labels

• Sends all the current information in the cursor and mouseover labels. Useful if you just set the cursor or if the vertex information under the cursor just changed, and want to force an update of the information.

Anchor(send_spherical_point) send_spherical_point subjectName canonicalFileName origFileName

• Converts the cursor to a cross-subject spherical point, then remaps it to a different subject's surface, and writes it to their edit.dat cursor file, so that subject use the Read Cursor command to get this cursor. 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.

Anchor(send_to_subject) send_to_subject subjectName

• Calls send_sphericAnchor(curv_to_val)

curv_to_val

• Copies the curvature values into the first overlay values.

al_point with standard file names for canonicalFileName and origFileName.

Anchor(set_current_vertex_set) set_current_vertex_set field

• Sets the current vertex set (the one being displayed) to the named field. field should be one of the values in read_surface_vertex_set.

Anchor(show_flat_regions) show_flat_regions surfaceFileName threshold

• 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(show_surf) show_surf vertexSet

• Moves the specified vertex set into the main vertex set position. vertexSet is white, pial, or inflate.

Anchor(shrink) shrink numberOfSteps

• Inflates the surface by the number of steps given. numberOfSteps should be an integer.

Anchor(smooth_curv) smooth_curv numberOfSteps

• Smooths the curvature values by numberOfSteps, an integer

Anchor(stat_to_val) stat_to_val

• Copies the values of the stat field to the overlay value field.

Anchor(swap_vertex_fields) swap_vertex_fields field field

• A more general way of swaping vertex fields. field should be one of the following:

Anchor(transform_brain) transform_brain

• Recenters the brain.

Anchor(translate_brain_x) translate_brain_x distance

• Translates the view along the x axis. distance should be a floating point number and is in millimeters.

Anchor(translate_brain_y) translate_brain_y distance

• Translates the view along the x axis. distance should be a floating point number and is in millimeters.

Anchor(translate_brain_z) translate_brain_z distance

• Translates the view along the x axis. distance should be a floating point number and is in millimeters.

Anchor(undo_last_action) undo_last_action

• Undoes the last action.

Anchor(val_to_curv) val_to_curv

• Copies the first overlay values into the curvature values.

Anchor(val_to_mark) val_to_mark

• Will mark all vertices with overlay values greater than the overlay threshold.

Anchor(val_to_stat) val_to_stat

• Copies the values of the overlay value field to the stat field.

Anchor(write_binary_curv) write_binary_curv

• Saves the curvature values to a new file. Will read the file name from curv.

Anchor(write_binary_dipoles) write_binary_dipoles

• Write the dipoles to a file. Will read the file name from dip.

Anchor(write_binary_patch) write_binary_patch

• Saves the current surface as a patch. Will read the file name from patch.

Anchor(write_binary_sulc) write_binary_sulc

• Saves the sulcus values (if loaded in the curvature set) to a new file. Will read the file name from sulc.

Anchor(write_binary_surface) write_binary_surface

• Saves the surface to a new file. Will read the file name from outsurf.

Anchor(write_fieldsign) write_fieldsign

• Saves the field sign values to a new file. Will read the file name from fs.

Anchor(write_fsmask) write_fsmask

• Saves the field sign mask to a new file. Will read the file name from fm.

Anchor(write_labeled_vertices) write_labeled_vertices

• Saves all marked values to a label file. Will fill in the stat value of the file with the current overlay field's value. Will read the file name from label.

Anchor(write_really_matrix) write_really_matrix

• Writes the matrix used to transform the surface vertices. Reads the file name from subjtmpdir.

Anchor(write_view_matrix) write_view_matrix

• Write the current view matrix to a file. Reads the file name from subjtmpdir.

Anchor(write_vrml) write_vrml mode

• Writes a VRML version of the surface. Will read the file name from vrmlsurf. mode is 0 for pts, 1 for gray, and 2 for curv.

Index

Viewing Operations

[#align_sphere align_sphere] [#do_lighting_model do_lighting_model] [#draw_cursor draw_cursor] [#left_click left_click] [#make_lateral_view make_lateral_view] [#move_window move_window] [#redraw redraw] [#rotate_brain_x rotate_brain_x] [#rotate_brain_y rotate_brain_y] [#rotate_brain_z rotate_brain_z] [#scale_brain scale_brain] [#send_current_labels send_current_labels] [#show_flat_regions show_flat_regions] [#translate_brain_x translate_brain_x] [#translate_brain_y translate_brain_y] [#translate_brain_z translate_brain_z] [#read_really_matrix read_really_matrix] [#read_view_matrix read_view_matrix] [#really_center_brain really_center_brain] [#really_rotate_brain_x really_rotate_brain_x] [#really_rotate_brain_y really_rotate_brain_y] [#really_rotate_brain_z really_rotate_brain_z] [#really_scale_brain really_scale_brain] [#really_translate_brain really_translate_brain] [#resize_brain resize_brain] [#resize_window resize_window] [#restore_zero_position restore_zero_position] [#restore_initial_position restore_initial_position] [#transform_brain transform_brain] [#write_view_matrix write_view_matrix] [#write_really_matrix write_really_matrix]

I/O

[#func_load_timecourse func_load_timecourse] [#func_load_timecourse_offset func_load_timecourse_offset] [#labl_export_annotation labl_export_annotation] [#labl_import_annotation labl_import_annotation] [#labl_load labl_load] [#labl_load_color_table labl_load_color_table] [#labl_save labl_save] [#labl_save_all labl_save_all] [#read_annotations read_annotations] [#read_binary_curv read_binary_curv] [#read_binary_decimation read_binary_decimation] [#read_binary_dipoles read_binary_dipoles] [#read_binary_sulc read_binary_sulc] [#read_binary_surf read_binary_surf] [#read_binary_values read_binary_values] [#read_binary_values_frame read_binary_values_frame] [#read_binary_patch read_binary_patch] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] [#read_curv_to_val read_curv_to_val] [#read_fieldsign read_fieldsign] [#read_fsmask read_fsmask] [#read_imag_vals read_imag_vals] [#read_labeled_vertices read_labeled_vertices] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_surface_vertex_set read_surface_vertex_set] [#read_white_vertex_coordinates read_white_vertex_coordinates] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_write_dotw sclv_write_dotw] [#write_binary_curv write_binary_curv] [#write_binary_dipoles write_binary_dipoles] [#write_binary_patch write_binary_patch] [#write_binary_surface write_binary_surface] [#write_binary_sulc write_binary_sulc] [#write_fieldsign write_fieldsign] [#write_fsmask write_fsmask] [#write_labeled_vertices write_labeled_vertices] [#write_vrml write_vrml]

Curvature Operations

[#clear_curvature clear_curvature] [#compute_curvature compute_curvature] [#curv_to_val curv_to_val] [#fill_flood_from_cursor fill_flood_from_cursor] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#smooth_curv smooth_curv] [#val_to_curv val_to_curv]

Overlay Operations

[#curv_to_val curv_to_val] [#f_to_t f_to_t] [#fill_flood_from_cursor fill_flood_from_cursor] [#label_to_stat label_to_stat] [#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#sclv_copy_all_view_settings_from_current_field sclv_copy_all_view_settings_from_current_field] [#sclv_copy_view_settings_from_current_field sclv_copy_view_settings_from_current_field] [#sclv_copy_view_settings_from_field sclv_copy_view_settings_from_field] [#sclv_get_normalized_color_for_value sclv_get_normalized_color_for_value] [#sclv_load_label_value_file sclv_load_label_value_file] [#sclv_read_bfile_values sclv_read_bfile_values] [#sclv_read_binary_values sclv_read_binary_values] [#sclv_read_binary_values_frame sclv_read_binary_values_frame] [#sclv_read_from_dotw sclv_read_from_dotw] [#sclv_read_from_volume sclv_read_from_volume] [#sclv_send_current_field_info sclv_send_current_field_info] [#sclv_send_histogram sclv_send_histogram] [#sclv_set_current_field sclv_set_current_field] [#sclv_set_current_threshold_from_percentile sclv_set_current_threshold_from_percentile] [#sclv_set_current_threshold_using_fdr sclv_set_current_threshold_using_fdr] [#sclv_set_current_timepoint sclv_set_current_timepoint] [#sclv_set_overlay_alpha sclv_set_overlay_alpha] [#sclv_smooth sclv_smooth] [#sclv_write_dotw sclv_write_dotw] [#stat_to_val stat_to_val] [#swap_val_val2 swap_val_val2] [#val_to_curv val_to_curv] [#val_to_stat val_to_stat]

Vertex Operations

[#fill_flood_from_cursor fill_flood_from_cursor] [#find_orig_vertex_coordinates find_orig_vertex_coordinates] [#fix_nonzero_vals fix_nonzero_vals] [#flip_normals flip_normals] [#invert_face invert_face] [#invert_surface invert_surface] [#invert_vertex invert_vertex] [#read_canon_vertex_coordinates read_canon_vertex_coordinates] [#read_orig_vertex_coordinates read_orig_vertex_coordinates] [#read_pial_vertex_coordinates read_pial_vertex_coordinates] [#read_surface_vertex_set read_surface_vertex_set] [#read_white_vertex_coordinates read_white_vertex_coordinates] [#set_current_vertex_set set_current_vertex_set] [#show_surf show_surf] [#shrink shrink] [#swap_vertex_fields swap_vertex_fields]

Cursor Operations

[#draw_cursor draw_cursor] [#resend_to_subject resend_to_subject] [#select_orig_vertex_coordinates select_orig_vertex_coordinates] [#select_talairach_point select_talairach_point] [#select_vertex_by_vno select_vertex_by_vno] [#send_spherical_point send_spherical_point] [#send_to_subject send_to_subject]

Ripping and Cutting Operations

[#clear_ripflags clear_ripflags] [#cut_line cut_line] [#cut_plane cut_plane] [#dilate_ripped dilate_ripped] [#restore_ripflags restore_ripflags] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] [#undo_last_action undo_last_action]

Reporting Information

[#dump_vertex dump_vertex] [#get_selected_path_vnos get_selected_path_vnos] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#plot_curv plot_curv]

Screen Shots

[#save_rgb save_rgb] [#save_rgb_cmp_frame save_rgb_cmp_frame] [#save_tiff save_tiff]

Marking Operations

[#clear_all_vertex_marks clear_all_vertex_marks] [#clear_vertex_marks clear_vertex_marks] [#close_marked_vertices close_marked_vertices] [#get_selected_path_vnos get_selected_path_vnos] [#labl_mark_vertices labl_mark_vertices] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] [#mark_annotation mark_annotation] [#mark_contiguous_vertices_over_thresh mark_contiguous_vertices_over_thresh] [#mark_contiguous_vertices_with_similar_curvature mark_contiguous_vertices_with_similar_curvature] [#mark_face mark_face] [#mark_faces mark_faces] [#mark_vertex mark_vertex] [#rip_all_vertices_except_contiguous_upripped rip_all_vertices_except_contiguous_upripped] [#val_to_mark val_to_mark]

Label Operations

[#label_to_stat label_to_stat] [#labl_dilate labl_dilate] [#labl_erode labl_erode] [#labl_export_annotation labl_export_annotation] [#labl_import_annotation labl_import_annotation] [#labl_load labl_load] [#labl_load_color_table labl_load_color_table] [#labl_mark_vertices labl_mark_vertices] [#labl_new_from_marked_vertices labl_new_from_marked_vertices] [#labl_print_list labl_print_list] [#labl_print_table labl_print_table] [#labl_remove labl_remove] [#labl_remove_all labl_remove_all] [#labl_save labl_save] [#labl_save_all labl_save_all] [#labl_select labl_select] [#labl_set_color labl_set_color] [#labl_set_info labl_set_info] [#labl_set_name_from_table labl_set_name_from_table] [#labl_select_label_by_vno labl_select_label_by_vno] [#mask_label mask_label] [#send_current_labels send_current_labels]

Time Courses

[#func_clear_selection func_clear_selection] [#func_graph_timecourse_selection func_graph_timecourse_selection] [#func_load_timecourse func_load_timecourse] [#func_load_timecourse_offset func_load_timecourse_offset] [#func_print_timecourse_selection func_print_timecourse_selection] [#func_select_label func_select_label] [#func_select_marked_vertices func_select_marked_vertices]

Paths

[#path_new_path_from_marked_vertices path_new_path_from_marked_vertices] [#path_remove_selected_path path_remove_selected_path] [#path_select path_select]

Unsupported Functions

These commands are legacy functions that aren't documented well enough to be dependable. Because some older scripts still use them, they are documented here for completion. Use of them is not suggested nor supported.

Commands

Anchor(add_subject_to_average_curvim) add_subject_to_average_curvim subjectName morphSubdirectory

Anchor(clear_all_vertex_cursor) clear_all_vertex_cursor

Anchor(compute_angles) compute_angles

Anchor(compute_CMF) compute_CMF

Anchor(compute_cortical_thickness) compute_cortical_thickness

Anchor(compute_fieldsign) compute_fieldsign

Anchor(compute_pval_fwd) compute_pval_fwd pvalThreshold

• pvalThreshold is a floating point number.

Anchor(compute_pval_inv) compute_pval_inv

Anchor(compute_select_fwd) compute_select_fwd maximumDistance

maximumDistance is a floating point number in millimeters.

Anchor(compute_timecourses) compute_timecourses

Anchor(curv_shrink_to_fill) curv_shrink_to_fill numberOfSteps

Anchor(curv_to_curvim) curv_to_curvim

Anchor(curvim_to_second_surface) curvim_to_second_surface

Anchor(curvim_to_surface) curvim_to_surface

Anchor(deconvolve_weights) deconvolve_weights weightFileName scaleFileName

Anchor(draw_all_cursor) draw_all_cursor

Anchor(draw_all_vertex_cursor) draw_all_vertex_cursor

Anchor(draw_curvature_line) draw_curvature_line

Anchor(draw_fundus) draw_fundus

Anchor(draw_radius) draw_radius

Anchor(draw_theta) draw_theta

Anchor(draw_vector) draw_vector fileName

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

Anchor(ellipsoid_morph) ellipsoid_morph numberOfSteps rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance

• numberOfSteps is an integer. All distances are in millimeters and should be millimeters.

Anchor(ellipsoid_project) ellipsoid_project rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance

• All distances are in millimeters and should be millimeters.

Anchor(ellipsoid_shrink) ellipsoid_shrink numberOfSteps radius

• radius is in millimeters.

Anchor(ellipsoid_shrink_bug) ellipsoid_shrink_bug numberOfSteps radius length

• radius and length is in millimeters.

Anchor(f_to_p) f_to_p DOFnumerator DOFdenominator

Anchor(flatten) flatten

• Reads the file name from subjtmpdir.

Anchor(fill_second_surface) fill_second_surface

Anchor(filter_recs) filter_recs

Anchor(load_gcsa) load_gcsa fileName

Anchor(load_vals_from_sol) load_vals_from_sol tmid dt condition

• 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

• condition is an integer.

Anchor(make_lateral_view_second) make_lateral_view_second

Anchor(normalize_area) normalize_area

Anchor(normalize_binary_curv) normalize_binary_curv

Anchor(normalize_inverse) normalize_inverse

Anchor(normalize_second_binary_curv) normalize_second_binary_curv

Anchor(normalize_time_courses) normalize_time_courses type

• 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(open_window) open_window

Anchor(orient_sphere) orient_sphere

Anchor(plot_all_time_courses) plot_all_time_courses

Anchor(plot_marked) plot_marked fileName

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

Anchor(put_retinotopy_stats_in_vals) put_retinotopy_stats_in_vals

• Calculates retinotopy values at each vertex and stores them in the first overlay layer.

Anchor(read_and_color_labeled_vertices) read_and_color_labeled_vertices red green blue

• Sets the meshr,g,b values and calls read_labeled_vertices. The colors are integers from 0-254.

Anchor(read_and_smooth_parcellation) read_and_smooth_parcellation parcellationFileName colorTableFileName soapBubbleIterations modeFilterIterations

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

Anchor(read_annotated_image) read_annotated_image

• Will read the file from annot.

Anchor(read_curv_images) read_curv_images

• Loads files into the curvim array.

Anchor(read_disc) read_disc subjectName

Anchor(read_iop) read_iop fileName dipoleFileNumber

Anchor(read_ncov) read_ncov fileName

Anchor(read_parcellation) read_parcellation parcellationFileName colorTableFileName

• Reads and smooths a parcellation file into the annotation field. This is different than importing a parcellation file in as a series of labels; this parcellation goes right into surface value fields.

Anchor(read_plot_list) read_plot_list fileName

Anchor(read_rec) read_rec fileName

Anchor(read_second_binary_curv) read_second_binary_curv

• Reads a curvature file into mris2. Reads the file name from targcurv.

Anchor(read_second_binary_surf) read_second_binary_surf

• Reads mris2. Reads the file name from targsurf.

Anchor(read_soltimecourse) read_soltimecourse fileName

Anchor(read_stds) read_stds conditionNumber

• Reads a series of sigvarCOND-?h.w files and a sigavgCOND.dof file into the val field.

Anchor(read_surf) read_surf fileName

• Reads only vertex positions from a file into the main surface, overwriting the original positions.

Anchor(read_vertex_list) read_vertex_list fileName

Anchor(really_align_brain) really_align_brain

• Aligns first surface to second.

Anchor(really_center_second_brain) really_center_second_brain

• Works on the second mris.

Anchor(redraw_second) redraw_second

• Draws second surface.

Anchor(remove_triangle_links) remove_triangle_links

• Calls MRISremoveTriangleLinks.

Anchor(restore_surf) restore_surf

• Restores the vertex positions in the temp position to the main position.

Anchor(save_surf) save_surf

• Saves the vertex positions in the main position to the temp position.

Anchor(sclv_read_from_dotw_frame) sclv_read_from_dotw_frame

• This seems to load in a surface full of values, and then individual values, from a file.

Anchor(second_surface_curv_to_curvim) second_surface_curv_to_curvim

• Works on mris2.

Anchor(shift_values) shift_values

• Places the values from the first overlay field into the second.

Anchor(smooth_curvim) smooth_curvim numberOfSteps

Anchor(smooth_curvim_sparse) smooth_curvim_sparse numberOfSteps

Anchor(sphere_shrink) sphere_shrink numberOfSteps radius

• radius is in millimeters.

Anchor(smooth_fs) smooth_fs numberOfSteps

• Smooths the field sign values by numberOfSteps, an integer.

Anchor(smooth_val) smooth_val numberOfSteps

• sclv_smooth is used instead.

Anchor(smooth_val_sparse) smooth_val_sparse numberOfSteps

Anchor(sol_plot) sol_plot timePoint plotType

• Uses the dlat value in computing the range.

Anchor(subsample_dist) subsample_dist spacing

• Used in decimation. Calls MRISsubsampleDist. spacing is an integer.

Anchor(subsample_orient) subsample_orient spacing

• Used in decimation. spacing is an integer.

Anchor(swap_buffers) swap_buffers

Anchor(swap_curv) swap_curv

• Swaps the curv and curvbak fields.

Anchor(swap_stat_val) swap_stat_val

• Swaps the values in the first overlay field and the fifth.

Anchor(swap_val_val2) swap_val_val2

• Swaps the values in the first overlay field and the second.

Anchor(swap_values) swap_values

• Swaps the values in the first overlay field and the second.

Anchor(t_to_p) t_to_p DOF

Anchor(to_double_buffer) to_double_buffer

Anchor(to_single_buffer) to_single_buffer

Anchor(twocond) twocond condition condition

• Both conditions are integers.

Anchor(write_binary_areas) write_binary_areas

• Calls MRISwriteArea. Will read the file name from area.

Anchor(write_binary_decimation) write_binary_decimation

• Calls MRISwriteDecimation. Will read the file name from dec.

Anchor(write_binary_values) write_binary_values

• Calls MRISwriteValues. Will read the file name from val.

Anchor(write_curv_images) write_curv_images

• Will read the file name from targcurvim.

Anchor(write_decimation) write_decimation

• Will read the file name from dec.

Anchor(write_dipoles) write_dipoles

• Will read the file name from dip.

Anchor(write_fill_images) write_fill_images

Anchor(write_subsample) write_subsample

• Writes an ASCII file. Will read the file name from fs.

Index

[#add_subject_to_average_curvim add_subject_to_average_curvim] [#clear_all_vertex_cursor clear_all_vertex_cursor] [#compute_angles compute_angles] [#compute_CMF compute_CMF] [#compute_cortical_thickness compute_cortical_thickness] [#compute_fieldsign compute_fieldsign] [#compute_pval_fwd compute_pval_fwd] [#compute_pval_inv compute_pval_inv] [#compute_select_fwd compute_select_fwd] [#compute_timecourses compute_timecourses] [#curv_shrink_to_fill curv_shrink_to_fill] [#curv_to_curvim curv_to_curvim] [#curvim_to_second_surface curvim_to_second_surface] [#curvim_to_surface curvim_to_surface] [#deconvolve_weights deconvolve_weights] [#draw_all_cursor draw_all_cursor] [#draw_all_vertex_cursor draw_all_vertex_cursor] [#draw_curvature_line draw_curvature_line] [#draw_fundus draw_fundus] [#draw_radius draw_radius] [#draw_theta draw_theta] [#draw_vector draw_vector] [#ellipsoid_morph ellipsoid_morph] [#ellipsoid_project ellipsoid_project] [#ellipsoid_shrink ellipsoid_shrink] [#ellipsoid_shrink_bug ellipsoid_shrink_bug] [#f_to_p f_to_p] [#flatten flatten] [#fill_second_surface fill_second_surface] [#filter_recs filter_recs] [#load_gcsa load_gcsa] [#load_vals_from_sol load_vals_from_sol] [#load_var_from_sol load_var_from_sol] [#make_lateral_view_second make_lateral_view_second] [#normalize_area normalize_area] [#normalize_binary_curv normalize_binary_curv] [#normalize_inverse normalize_inverse] [#normalize_second_binary_curv normalize_second_binary_curv] [#normalize_time_courses normalize_time_courses] [#open_window open_window] [#orient_sphere orient_sphere] [#plot_all_time_courses plot_all_time_courses] [#plot_marked plot_marked] [#put_retinotopy_stats_in_vals put_retinotopy_stats_in_vals] [#read_and_color_labeled_vertices read_and_color_labeled_vertices] [#read_and_smooth_parcellation read_and_smooth_parcellation] [#read_annotated_image read_annotated_image] [#read_curv_images read_curv_images] [#read_disc read_disc] [#read_iop read_iop] [#read_ncov read_ncov] [#read_parcellation read_parcellation] [#read_plot_list read_plot_list] [#read_rec read_rec] [#read_second_binary_surf read_second_binary_surf] [#read_second_binary_curv read_second_binary_curv] [#read_soltimecourse read_soltimecourse] [#read_stds read_stds] [#read_surf read_surf] [#read_vertex_list read_vertex_list] [#really_align_brain really_align_brain] [#really_center_second_brain really_center_second_brain] [#redraw_second redraw_second] [#remove_triangle_links remove_triangle_links] [#restore_surf restore_surf] [#save_surf save_surf] [#sclv_read_from_dotw_frame sclv_read_from_dotw_frame] [#second_surface_curv_to_curvim second_surface_curv_to_curvim] [#shift_values shift_values] [#smooth_curvim smooth_curvim] [#smooth_curvim_sparse smooth_curvim_sparse] [#sphere_shrink sphere_shrink] [#smooth_fs smooth_fs] [#smooth_val smooth_val] [#smooth_val_sparse smooth_val_sparse] [#sol_plot sol_plot] [#subsample_dist subsample_dist] [#subsample_orient subsample_orient] [#swap_buffers swap_buffers] [#swap_curv swap_curv] [#swap_stat_val swap_stat_val] [#swap_stat_val2 swap_stat_val2] [#swap_values swap_values] [#t_to_p t_to_p] [#to_single_buffer to_single_buffer] [#to_double_buffer to_double_buffer] [#twocond twocond] [#write_binary_areas write_binary_areas] [#write_binary_decimation write_binary_decimation] [#write_binary_values write_binary_values] [#write_curv_images write_curv_images] [#write_decimation write_decimation] [#write_dipoles write_dipoles] [#write_fill_images write_fill_images] [#write_subsample write_subsample]