||Up to TkSurferGuide||Back to [[../TkSurferScriptingReference| TkSurferScriptingReference]]||Continue to [[TkSurferGuide/TkSurferReference| TkSurferReference]]|| = 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. == Variables == These variables are used to turn on and off certain display characteristics. The way to set a flag is: {{{ set gaLinkedVars(VARIABLENAME) VALUE SendLinkedVarGroup GROUP }}} Here is a table listing the variables, valid values, group names, and functionality. ||Variable Name||Valid Values||Group||GUI Location||Description|| ||vertexset||0-4||view||View->Surface Configuration||Use to set the current visible surface configuration. Use 0 for Main, 1 for Inflated, 2 for White, 3 for Pial, and 4 for Original.|| ||currentvaluefield||0-8||view||View->Overlay Layer||Sets the current overlay layer. Should be followed with a call to '''Set``Overlay``Field'''.|| ||labelstyle||0-1||label||View->Label Style||Sets the label drawing style. Use 0 for filled and 1 for outline.|| ||redrawlockflag||0,1||redrawlock||View->Auto-redraw||Sets the auto-redraw flag.|| ||curvflag||0,1||view||View->Curvature||Controls curvature display.|| ||overlayflag||0,1||view||View->Overlay||Controls overlay layer display.|| ||drawlabelflag||0,1||label||View->Labels||Controls label display.|| ||labels_before_overlay_flag||0,1||label||View->Labels under Overlay||Controls whether labels are drwn under the overlay.|| ||scalebarflag||0,1||view||View->Scale Bar||Controls scale bar display.|| ||colscalebarflag||0,1||view||View->Color Scale Bar||Controls the overlay color scale bar display.|| ||verticesflag||0,1||view||View->Wireframe Overlay||Controls the wireframe display.|| ||drawcursorflag||0,1||view||View->Cursor||Controls the cursor display.|| ||light0||0-1 (floating)||scene||View->Configure->Lighting||Sets the first light value.|| ||light1||0-1 (floating)||scene||View->Configure->Lighting||Sets the second light value.|| ||light2||0-1 (floating)||scene||View->Configure->Lighting||Sets the third light value.|| ||light3||0-1 (floating)||scene||View->Configure->Lighting||Sets the fourth light value.|| ||offset||0-1 (floating)||scene||View->Configure->Lighting||Sets the ambient light value.|| ||fthresh||floating||overlay||View->Configure->Overlay||Sets the overlay threshold minimum.|| ||fmid||floating||overlay||View->Configure->Overlay||Sets the overlay threshold midpoint.|| ||fslope||floating||overlay||View->Configure->Overlay||Sets the overlay threshold slope.|| ||falpha||0-1 (floating)||overlay||View->Configure->Overlay||Sets the overlay alpha value.|| ||ftimepoint||integer||overlay||View->Configure->Overlay||Sets the time point in the current overlay layer.|| ||fcondition||integer||overlay||View->Configure->Overlay||Sets the condition in the current overlay layer.|| ||colscale||0-8||overlay||View->Configure->Overlay||Sets the overlay color scale type. Use 0 for Color Wheel, 1 for Heat, 4 for Two Cond G/R, 6 for Blue Red, 7 for Green Red, 8 for RYGB Wheel|| ||truncphaseflag||0,1||overlay||View->Configure->Overlay||Sets the overlay Truncate flag.|| ||invphaseflag||0,1||overlay||View->Configure->Overlay||Sets the overlay Inverse flag.|| ||complexvalflag||0,1||overlay||View->Configure->Overlay||Sets the Complex flag.|| ||ignorezeroesinhistogramflag||0,1||overlay||View->Configure->Overlay||Sets the Ignore Zeroes in Histogram flag|| ||cmid||floating||curvature||View->Configure->Curvature||Sets the midpoint value for the curvature display.|| ||forcegraycurvatureflag||0,1||curvature||View->Configure->Curvature||Controls the binary gray curvature display.|| == Commands == Functions arguments are listed by their name followed by their arguments. Arguments in square brackets are optional. <> ''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). <> ''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). <> ''clear_curvature'' Sets all curvature values to 0. <> ''clear_ripflags'' Unrips all vertices. <> ''clear_vertex_marks'' Unmarks the marked vertices. <> ''close_marked_vertices'' Adds the first marked vertex to the end of the list of marked vertices. <> ''compute_curvature'' Computes the curvature based on vertex positions. <> ''curv_to_val'' Copies the curvature values into the first overlay values. <> ''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. <> ''cut_plane'' Cuts a plane based on four marked vertices: three to define the plane, and one to indicate which area to not cut. <> ''dilate_ripped'' Dilates ripped areas, increasing their size by a vertex. <> ''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. <> ''draw_cursor'' '''''vertexNumber on''''' Draws the specified vertex in blue if '''on,''' or in the background color if not '''on'''. <> ''dump_vertex'' '''''vertexNumber''''' Prints information about the specified vertex. '''vertexNumber''' is an integer. <> ''f_to_t'' Squares and takes the absolute value for every overlay value field in the vertices. <> ''find_orig_vertex_coordinates'' Performs the '''Save Cursor''' function. Writes the current cursor location to the ''edit.dat'' file. <> ''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. <> ''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. <> ''func_clear_selection'' Clears the functional time course 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. <> ''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. <> ''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. <> ''func_print_timecourse_selection'' '''''fileName''''' Prints a text file summarizing the data selected in the functional time course. <> ''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. <> ''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. <> ''invert_face'' '''''faceNumber''''' Inverts the face normal at the numbered face. '''faceNumber''' is an integer. <> ''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: ||0||No action, just mark filled vertices. '''argument''' is ignored.|| ||1||Make the filled vertices a new label. '''argument''' is ignored.|| ||2||Add the filled vertices to an existing label. '''argument''' should be the index of the label to add vertices to.|| ||3||Remove the filled vertices from an existing label. '''argument''' should be the index of the label to remove from.|| <> ''get_marked_vnos'' Returns a list of marked vertices. <> ''get_selected_path_vnos'' Returns a list of vertices in the selected path. <> ''invert_surface'' Inverts the vertex normals for all unripped vertices in the surface, but not the faces. <> ''invert_vertex'' '''''vertexNumber''''' Inverts the vertex normal at the numbered vertex. '''vertexNumber''' is an integer. <> ''label_to_stat'' '''''overlayField''''' Creates a new overlay layer with the values in the current label in overlay field '''overlayField'''. <> ''labl_dilate'' '''''label''''' Expands a label by adding all vertices immediately adjacent to the label. '''label''' should be a valid label index. <> ''labl_erode'' '''''label''''' Shrinks a label by excluding all border vertices in the label. '''label''' should be a valid label index. <> ''labl_export_annotation'' '''''fileName''''' Exports all labels marked as structures to an annotation. <> ''labl_import_annotation'' '''''fileName''''' Important an annotation file as a series of label. <> ''labl_load'' '''''fileName''''' Loads the label in '''fileName''' and adds it to the Labels window. <> ''labl_load_color_table'' '''''fileName''''' Loads a color table for labels to use from '''fileName'''. <> ''labl_mark_vertices'' '''''label''''' Marks the vertices in a label. '''label''' should be a valid label index. <> ''labl_new_from_marked_vertices'' Creates a new label from the marked vertices. <> ''labl_print_list'' Prints a list of label information to the shell <> ''labl_print_table'' Prints the color table to the shell. <> ''labl_remove'' '''''label''''' Deletes a label. '''label''' should be a valid label index. <> ''labl_remove_all'' Deletes all labels. <> ''labl_save'' '''''label fileName''''' Saves a label to '''fileName'''. '''label''' should be a valid label index. <> ''labl_save_all'' '''''prefix''''' Saves all labels with a given prefix directory location. <> ''labl_select'' '''''label''''' Marks the vertices in a label. '''label''' should be a valid label index. <> ''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. <> ''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. <> ''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. <> ''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. <> ''left_click'' '''''x y''''' Simulates a click at the given window position. '''x''' and '''y''' should be integers. <> ''make_lateral_view'' Changes the view to show the surface laterally. <> ''mark_annotation'' '''''vertexNumber''''' Will mark all vertices with the same annotation value as the annotation value at the specified vertex. '''vertexNumber''' is an integer. <> ''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.) <> ''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.) <> ''mark_face'' '''''faceNumber''''' Marks all vertices in the specified face. '''faceNumber''' is an integer. <> ''mark_faces'' '''''vertexNumber''''' Marks all vertices in the face to which the specified vertex belongs. '''vertexNumber''' is an integer. <> ''mark_vertex'' '''''vertexNumber on''''' Marks or unmarks a specified vertex. '''vertexNumber''' is an integer, and '''on''' is 0 for off and 1 for on. <> ''mask_label'' '''''labelFileName''''' This reads and marks a label file, and then for every vertex not marked, clears the overlay values. <> ''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. <> ''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. <> ''path_remove_selected_path'' Deletes the selected path. <> ''path_select'' '''''path''''' Selects the specified path. '''path''' should be a valid path index. <> ''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. <> ''print_nearest_vertex_to_talairach_point'' '''''x''''' '''''y''''' '''''z''''' '''*''' Prints the nearest vertex to the specified talairach point x, y, z '''''only available in the internal dev version''''' <> ''read_annotations'' '''''fileName''''' Deprecated, replaced by ''labl_import_annotation''. '''fileName''' is an annotation file name, usually ending in .annot. <> ''read_binary_curv'' Loads a curvature file into the surface. Reads the file name from '''curv'''. <> ''read_binary_decimation'' Reads decimation values onto the surface from a file. Reads the file name from '''dec'''. <> ''read_binary_dipoles'' Reads dipole balues onto the surface from a file. Reads the file name from '''dip'''. <> ''read_binary_patch'' Reads a patch file into the surface. Will read the file name from '''patch'''. <> ''read_binary_sulc'' Reads a sulcus file into the curvature display. Reads the file name from '''sulc'''. <> ''read_binary_surf'' Loads the main surface from a surface file. Reads the file name from '''insurf'''. <> ''read_binary_values'' Deprecated, replaced by ''sclv_read_from_dotw''. Will read the value file from '''val'''. <> ''read_binary_values_frame'' Deprecated, replaced by ''sclv_read_from_dotw_frame''. Will read the value file from '''val'''. <> ''read_canon_vertex_coordinates'' '''''fileName''''' Reads the vertex coordinates from a file into the canonical vertex set. <> ''read_curv_to_val'' '''''fileName''''' Reads a curvature file into the first overlay layer. <> ''read_fieldsign'' Reads field sign values from a file. Will read the file name from '''fs'''. <> ''read_fsmask'' Reads the field sign mask from a file. Will read the file name from '''fm'''. <> ''read_imag_vals'' '''''fileName''''' Reads imaginary values from '''fileName'''. <> ''read_labeled_vertices'' Deprecated, replaced by ''labl_load''. Will read the file name from '''label'''. <> ''read_orig_vertex_coordinates'' Reads the vertex coordinates from a file into the orig vertex set. Reads the file name from '''origcoords'''. <> ''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. <> ''read_really_matrix'' Reads a matrix to transform the surface vertices. Reads the file name from '''subjtmpdir'''. <> ''read_surface_vertex_set'' '''''field fileName''''' Reads a set of vertices from the fle in '''fileName'''. '''field''' should be one of the following: ||0||Main vertices|| ||1||Inflated vertices|| ||2||White vertices|| ||3||Pial vertices|| ||4||Orig vertices|| <> ''read_view_matrix'' Reads a view matrix from a file. Reads the file name from '''subjtmpdir'''. <> ''read_white_vertex_coordinates'' Reads the vertex coordinates from a file called ''?h.white'' where ? is the current hemisphere into the original vertex set. <> ''really_center_brain'' Translates the surface coordinates to an average of all vertex coordinates. <> ''really_rotate_brain_x'' '''''degrees''''' Rotates the surface vertices around the x axis. '''degrees''' is a floating point number. <> ''really_rotate_brain_y'' '''''degrees''''' Rotates the surface vertices around the y axis. '''degrees''' is a floating point number. <> ''really_rotate_brain_z'' '''''degrees''''' Rotates the surface vertices around the z axis. '''degrees''' is a floating point number. <> ''really_translate_brain'' '''''rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance''''' Translates the surface vertices along the specified axes. All distances are in millimeters and can be floating point. <> ''redraw'' Redraws the graphics window. It is necessary to call this after using other script commands to change the viewing state. <> ''resend_to_subject'' Calls ''send_to_subject'' with the sam subject name used in the previous send_to_subject call. <> ''resize_brain'' Scales the brain according to the surface area to total area ratio. <> ''resize_window'' '''''size''''' Resizes the graphics window. '''size''' is an integer. The new window size will be sqaure with '''''size''''' x '''''sizedimensions'''''. <> ''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. <> ''restore_initial_position'' Restores the view to a medial view. <> ''restore_zero_position'' Restores the view to a medial view. <> ''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.) <> ''rotate_brain_x'' '''''degrees''''' Rotates the view around the x axis. '''degrees''' should be a floating point number. <> ''rotate_brain_y'' '''''degrees''''' Rotates the view around the y axis. '''degrees''' should be a floating point number. <> ''rotate_brain_z'' '''''degrees''''' Rotates the view around the z axis. '''degrees''' should be a floating point number. <> ''save_rgb'' Saves the contents of the view to a file in RGB format. Reads the file name from '''rgb'''. <> ''save_rgb_cmp_frame'' Reads the file name from '''rgb'''. Write an rgb frame file to be composed into a movie later. <> ''save_tiff'' '''''fileName''''' Saves the current graphics contents as a TIFF file. <> ''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. <> ''sclv_copy_all_view_settings_from_current_field'' Copies the settings from the current overlay to all other overlay layers. <> ''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''. <> ''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''. <> ''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. <> ''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. <> ''sclv_read_bfile_values'' Deprecated, replaced by ''sclv_read_from_volume''. <> ''sclv_read_binary_values'' Deprecated, replaced by ''sclv_read_from_dotw''. <> ''sclv_read_binary_values_frame'' '''''fileName field''''' Deprecated, replaced by ''sclv_read_from_dotw_frame''. <> ''sclv_read_from_dotw'' '''''fileName field''''' Reads an overlay layer from the file specified in dotw format. '''field''' should be one of the following: ||'''field'''||Vertex field name||Description|| ||0||val||Overlay layer 0|| ||1||val2||Overlay layer 1|| ||2||valbak||Overlay layer 2|| ||3||val2bak||Overlay layer 3|| ||4||stat||Overlay layer 4|| ||5||imag_val||Overlay layer 5|| ||6||mean||Overlay layer 6|| ||7||mean_imag||Overlay layer 7|| ||8||std_error||Overlay layer 8|| <> ''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: ||0||Get registration from a file, and specify file in '''regitrationFileName'''|| ||1||Look for a file named {{{register.dat}}} in the same directory as the volume.|| ||2||Calculate an identity registration using the orig volume (must be present in subject's {{{mri}}} directory.|| If the '''registrationType''' is 0, then '''registrationFileName''' must be provided, otherwise it can be omitted. <> ''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''. <> ''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''. <> ''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''. <> ''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 0-1 representing percentages which will be mapped to overlay values to be used to set the threshold (for example: .92 .925 .99) <> ''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. <> ''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. <> ''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. <> ''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''. <> ''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''. <> ''select_orig_vertex_coordinates'' Performs the '''Read Cursor''' function. Reads the cursor location from the ''edit.dat'' file. <> ''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. <> ''select_vertex_by_vno'' '''''vertexNumber''''' Selects the given vertex as the cursor. '''vertexNumber''' is an integer. <> ''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. <> ''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.''' <> ''send_to_subject'' '''''subjectName''''' Calls ''send_spheric<> ''curv_to_val'' Copies the curvature values into the first overlay values. al_point'' with standard file names for '''canonicalFileName''' and '''origFileName'''. <> ''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''. <> ''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. <> ''show_surf'' '''''vertexSet''''' Moves the specified vertex set into the main vertex set position. '''vertexSet''' is white, pial, or inflate. <> ''shrink'' '''''numberOfSteps''''' Inflates the surface by the number of steps given. '''numberOfSteps''' should be an integer. <> ''smooth_curv'' '''''numberOfSteps''''' Smooths the curvature values by '''numberOfSteps''', an integer <> ''stat_to_val'' Copies the values of the stat field to the overlay value field. <> ''swap_vertex_fields'' '''''field field''''' A more general way of swaping vertex fields. '''field''' should be one of the following: ||'''field'''||Vertex field name||Description|| ||0||curv||Curvature display|| ||1||curvbak||Backup curvature (not displayed|| ||2||val||Overlay layer 0|| ||3||imag_val||Overlay layer 5|| ||4||val2||Overlay layer 1|| ||5||valbak||Overlay layer 2|| ||6||val2bak||Overlay layer 3|| ||7||stat||Overlay layer 4|| <> ''transform_brain'' Recenters the brain. <> ''translate_brain_x'' '''''distance''''' Translates the view along the x axis. '''distance''' should be a floating point number and is in millimeters. <> ''translate_brain_y'' '''''distance''''' Translates the view along the x axis. '''distance''' should be a floating point number and is in millimeters. <> ''translate_brain_z'' '''''distance''''' Translates the view along the x axis. '''distance''' should be a floating point number and is in millimeters. <> ''undo_last_action'' Undoes the last action. <> ''val_to_curv'' Copies the first overlay values into the curvature values. <> ''val_to_mark'' Will mark all vertices with overlay values greater than the overlay threshold. <> ''val_to_stat'' Copies the values of the overlay value field to the stat field. <> ''write_binary_curv'' Saves the curvature values to a new file. Will read the file name from '''curv'''. <> ''write_binary_dipoles'' Write the dipoles to a file. Will read the file name from '''dip'''. <> ''write_binary_patch'' Saves the current surface as a patch. Will read the file name from '''patch'''. <> ''write_binary_sulc'' Saves the sulcus values (if loaded in the curvature set) to a new file. Will read the file name from '''sulc'''. <> ''write_binary_surface'' Saves the surface to a new file. Will read the file name from '''outsurf'''. <> ''write_fieldsign'' Saves the field sign values to a new file. Will read the file name from '''fs'''. <> ''write_fsmask'' Saves the field sign mask to a new file. Will read the file name from '''fm'''. <> ''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'''. <> ''write_really_matrix'' Writes the matrix used to transform the surface vertices. Reads the file name from '''subjtmpdir'''. <> ''write_view_matrix'' Write the current view matrix to a file. Reads the file name from '''subjtmpdir'''. <> ''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 == <> ''add_subject_to_average_curvim'' '''''subjectName morphSubdirectory''''' <> ''clear_all_vertex_cursor'' <> ''compute_angles'' <> ''compute_CMF'' <> ''compute_cortical_thickness'' <> ''compute_fieldsign'' <> ''compute_pval_fwd'' '''''pvalThreshold''''' '''pvalThreshold''' is a floating point number. <> ''compute_pval_inv'' <> ''compute_select_fwd'' '''''maximumDistance''''' '''maximumDistance''' is a floating point number in millimeters. <> ''compute_timecourses'' <> ''curv_shrink_to_fill'' '''''numberOfSteps''''' <> ''curv_to_curvim'' <> ''curvim_to_second_surface'' <> ''curvim_to_surface'' <> ''deconvolve_weights'' '''''weightFileName scaleFileName''''' <> ''draw_all_cursor'' <> ''draw_all_vertex_cursor'' <> ''draw_curvature_line'' <> ''draw_fundus'' <> ''draw_radius'' <> ''draw_theta'' <> ''draw_vector'' '''''fileName''''' Reads an x/y vector from '''fileName''' and draws it to the screen. <> ''ellipsoid_morph'' '''''numberOfSteps rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance''''' '''numberOfSteps''' is an integer. All distances are in millimeters and should be millimeters. <> ''ellipsoid_project'' '''''rightLeftDistance anteriorPosteriorDistance superiorInferiorDistance''''' All distances are in millimeters and should be millimeters. <> ''ellipsoid_shrink'' '''''numberOfSteps radius''''' '''radius''' is in millimeters. <> ''ellipsoid_shrink_bug'' '''''numberOfSteps radius length''''' '''radius''' and '''length''' is in millimeters. <> ''f_to_p'' '''''DOFnumerator DOFdenominator''''' <> ''flatten'' Reads the file name from '''subjtmpdir'''. <> ''fill_second_surface'' <> ''filter_recs'' <> ''load_gcsa'' '''''fileName''''' <> ''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. <> ''load_var_from_sol'' '''''condition''''' '''condition''' is an integer. <> ''make_lateral_view_second'' <> ''normalize_area'' <> ''normalize_binary_curv'' <> ''normalize_inverse'' <> ''normalize_second_binary_curv'' <> ''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. <> ''open_window'' <> ''orient_sphere'' <> ''plot_all_time_courses'' <> ''plot_marked'' '''''fileName''''' Generates a summary file of data from all marked vertices in '''fileName'''. <> ''put_retinotopy_stats_in_vals'' Calculates retinotopy values at each vertex and stores them in the first overlay layer. <> ''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. <> ''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. <> ''read_annotated_image'' Will read the file from '''annot'''. <> ''read_curv_images'' Loads files into the curvim array. <> ''read_disc'' '''''subjectName''''' <> ''read_iop'' '''''fileName dipoleFileNumber''''' <> ''read_ncov'' '''''fileName''''' <> ''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. <> ''read_plot_list'' '''''fileName''''' <> ''read_rec'' '''''fileName''''' <> ''read_second_binary_curv'' Reads a curvature file into mris2. Reads the file name from '''targcurv'''. <> ''read_second_binary_surf'' Reads mris2. Reads the file name from '''targsurf'''. <> ''read_soltimecourse'' '''''fileName''''' <> ''read_stds'' '''''conditionNumber''''' Reads a series of sigvarCOND-?h.w files and a sigavgCOND.dof file into the val field. <> ''read_surf'' '''''fileName''''' Reads only vertex positions from a file into the main surface, overwriting the original positions. <> ''read_vertex_list'' '''''fileName''''' <> ''really_align_brain'' Aligns first surface to second. <> ''really_center_second_brain'' Works on the second mris. <> ''redraw_second'' Draws second surface. <> ''remove_triangle_links'' Calls MRI``Sremove``Triangle``Links. <> ''restore_surf'' Restores the vertex positions in the temp position to the main position. <> ''save_surf'' Saves the vertex positions in the main position to the temp position. <> ''sclv_read_from_dotw_frame'' This seems to load in a surface full of values, and then individual values, from a file. <> ''second_surface_curv_to_curvim'' Works on mris2. <> ''shift_values'' Places the values from the first overlay field into the second. <> ''smooth_curvim'' '''''numberOfSteps''''' <> ''smooth_curvim_sparse'' '''''numberOfSteps''''' <> ''sphere_shrink'' '''''numberOfSteps radius''''' '''radius''' is in millimeters. <> ''smooth_fs'' '''''numberOfSteps''''' Smooths the field sign values by '''numberOfSteps''', an integer. <> ''smooth_val'' '''''numberOfSteps''''' sclv_smooth is used instead. <> ''smooth_val_sparse'' '''''numberOfSteps''''' <> ''sol_plot'' '''''timePoint plotType''''' Uses the '''dlat''' value in computing the range. <> ''subsample_dist'' '''''spacing''''' Used in decimation. Calls MRI``Ssubsample``Dist. '''spacing''' is an integer. <> ''subsample_orient'' '''''spacing''''' Used in decimation. '''spacing''' is an integer. <> ''swap_buffers'' <> ''swap_curv'' Swaps the curv and curvbak fields. <> ''swap_stat_val'' Swaps the values in the first overlay field and the fifth. <> ''swap_val_val2'' Swaps the values in the first overlay field and the second. <> ''swap_values'' Swaps the values in the first overlay field and the second. <> ''t_to_p'' '''''DOF''''' <> ''to_double_buffer'' <> ''to_single_buffer'' <> ''twocond'' '''''condition condition''''' Both conditions are integers. <> ''write_binary_areas'' Calls MRI``Swrite``Area. Will read the file name from '''area'''. <> ''write_binary_decimation'' Calls MRI``Swrite``Decimation. Will read the file name from '''dec'''. <> ''write_binary_values'' Calls MRI``Swrite``Values. Will read the file name from '''val'''. <> ''write_curv_images'' Will read the file name from '''targcurvim'''. <> ''write_decimation'' Will read the file name from '''dec'''. <> ''write_dipoles'' Will read the file name from '''dip'''. <> ''write_fill_images'' <> ''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]] == Notes == * Any command with a `*` is only available in the internal dev version. If you need a copy of tksurfer with a command only available in the dev version, let the relevant people know