||Up to TkSurferGuide||Back to [[../TkSurferMouseCommands| TkSurferMouseCommands]]||

= Menus =

== File ==

|| '''Load Surface...''' || Loads the main surface information, including main surface configuration. ||
|| '''Load Surface Configuration...''' || Shows a submenu with commands for loading vertex configurations. ||
|| '''Save Surface''' || Saves the contents of the entire surface structure, overwriting the original file. ||
|| '''Save Surface As...''' || Saves the contents of the entire surface structure to a new file. ||
|| '''Load Overlay...''' || Loads a .w or binary volume file into an overlay layer. ||
|| '''Load Label Value File...''' || Loads a Label Value File into an overlay layer. ||
|| '''Save Overlay As...''' || Saves an overlay layer as a new .w file. ||
|| '''Load Time Course...''' || Loads a binary volume as a time course. ||
|| '''Curvature''' || Shows a submenu with options for loading and saving. ||
|| '''Patch''' || Shows a submenu with options for loading and saving. ||
|| '''Label''' || Shows a submenu with options for loading and saving. ||
|| '''Field Sign''' || Shows a submenu with options for loading and saving. ||
|| '''Field Mask''' || Shows a submenu with options for loading and saving. ||
|| '''Quit''' || Quits TkSurfer. ||

== Load Surface Configuration ==

|| '''Main Vertices''' || Loads the specified vertices from another surface file into the selected surface configuration. ||
|| '''Inflated Vertices''' ||
|| '''White Vertices''' ||
|| '''Pial Vertices'''||
|| '''Original Vertices''' ||

== Curvature ==

|| '''Load Curvature...''' || Loads a curvature file. ||
|| '''Save''' || Saves changes to the curvature, overwriting the original file. ||
|| '''Save Curvature As...''' || Saves the curvature into a new file. ||

== Patch ==

|| '''Load Patch...''' || Loads a patch file. ||
|| '''Save Patch''' || Saves changes to the patch, overwriting the original file. ||
|| '''Save Patch As...''' || Saves the patch into a new file. ||

== Label ==

|| '''Load Color Table...''' || Load a color table to be available in the Labels window. ||
|| '''Load Label...''' || Loads a label file. ||
|| '''Save Selected Label...''' || Saves the label into a new file. ||
|| '''Import Annotation...''' || Read an annotation file in as a series of labels. ||
|| '''Delete All Labels''' || Delete all labels on the surface. ||

== Field Sign ==

|| '''Load Field Sign...''' || Loads a field sign file. ||
|| '''Save Field Sign''' || Saves changes to the field sign, overwriting the original file. ||
|| '''Save Field Sign As...''' || Saves the field sign into a new file. ||

== Field Mask ==

|| '''Load Field Mask...''' || Loads a field mask file. ||
|| '''Save Field Mask''' || Saves changes to the field mask, overwriting the original file. ||
|| '''Save Field Mask As...''' || Saves the field mask into a new file. ||

== Edit ==

|| '''Undo''' || Undoes the cut. ||
|| '''Unmark All Vertices''' || Unmarks all vertices. Same as clicking with button 3 in the Graphics window. ||
|| '''Deselect Label''' || Deselects a label if one is selected. ||

== View ==

|| '''Tool Bars''' || Shows a submenu of available toolbars. Check or uncheck the toolbar in this submenu to show or hide the toolbar. ||
|| '''Information''' || Shows a submenu of available information area items such as coordinate labels. Check or uncheck the item in this submenu to show or hide the item. ||
|| '''Windows''' || Shows a submenu of available windows to bring to the top. ||
|| '''Configure''' || Shows a submenu of viewing characteristics that can be configured. ||
|| '''Surface Configuration''' || Shows a submenu of surface configurations. Check one to make the currently shown configuration. ||
|| '''Overlay Layer''' || Shows a submenu of overlay layers. Check one to make the currently shown layer. ||
|| '''Label Style''' || Shows a submenu of label styles. ||
|| '''Overlay Layer''' || Check to display the current overlay layer. ||
|| '''Auto-redraw''' || Check to always redraw the screen whenever it needs redrawing. ||
|| '''Curvature''' || Check to show the curvature overlay. ||
|| '''Overlay''' || Check to show the functional overlay. ||
|| '''Labels''' || Check to show labels. Also see the '''Label Style''' submenu. ||
|| '''Labels under Overlay''' || Check to draw labels underneath the overlay. Normal labels are drawn on top of the overlay. ||
|| '''Scale Bar''' || Check to display a scale bar in the window, showing the scale of 1mm. ||
|| '''Color Scale Bar''' || Check to display a color bar in the Display window, showing the range of colors in the current overlay color scale. ||
|| '''Wireframe Overlay''' || Check to display a wireframe view of the surface edges. ||
|| '''Cursor''' || Uncheck to hide the cursor display. ||

== Tool Bars ==

|| '''Main''' || Check to make the Main toolbar visible. This toolbar contains the following controls: Redraw View, Save Point, Goto Point, Main Surface, Inflated Surface, White Surface, Pial Surface, Orig Surface, Curvature, Overlay, Overlay Scale Bar, Labels, Filled Labels, Outlined Labels. ||
|| '''Navigation''' || Check to show the Navigation toolbar. This contains: Restore Home View, Rotate Surface (6), Translate Surface (4), Zoom Out, Zoom In. ||
|| '''Tools''' || Check to show the Tools toolbar. This contains: Cut Line, Cut Closed Line, Cut Plane, Fill Uncut Area, Restore Cuts, Draw Path, Draw Closed Path, Custom Fill, Erase Path, New Label From Marked, Mark Label, Erase Labe, Change Label Color. ||

== Information ==

|| '''Vertex Index''' || Check to show the nearest vertex index. ||
|| '''Distance''' || Check to show the distance in mm to the reported index. ||
|| '''Vertex RAS''' || Check to show the RAS coordinates of the vertex. ||
|| '''Vertex MNI Talairach''' || Check to show the MNI Talariach coordinates of the vertex. ||
|| '''Vertex Talairach''' || Check to show the Talairach coordinates of the vertex. ||
|| '''MRI Index''' || Check to show the anatomical index of the vertex in the anatomical volume for this subject. ||
|| '''Vertex Normal''' || Check to show the normal vector of the vertex. ||
|| '''Spherical X, Y, Z''' || Check to show the spherical coordinates. ||
|| '''Spherical Rho, Theta''' || Check to show the spherical rho and theta. ||
|| '''Curvature''' || Check to show the curvature value at the vertex. ||
|| '''Field Sign''' || Check to show the field sign value at the vertex. ||
|| '''Overlay Layer 1-9''' || Check to show the overlay layer value at the vertex. ||
|| '''Amplitude''' || Check to show the value at the vertex. ||
|| '''Angle''' || Check to show the value at the vertex. ||
|| '''Degree''' || Check to show the value at the vertex. ||
|| '''Label''' || Check to show the label at the vertex. ||
|| '''Annotation''' || Check to show the value at the vertex. ||
|| '''MRI Value''' || Check to show the MRI value at the associated anatomical location for this vertex. ||

== Configure ==

|| '''Lighting...''' || Opens a dialog box in which you can set the lighting parameters for the scene. ||
|| '''Overlay...''' || Opens a dialog in which you can change various characteristics of the overlay display. ||
|| '''Time Course...''' || Opens a dialog in which you can change various characteristics of the time course graph. ||
|| '''Curvature Display...''' || Opens a dialog in which you can change various characteristics of the curvature display. ||
|| '''Phase Encoded Data Display...''' || Opens a dialog in which you can change various characteristics of phase encoded data display. ||

== Surface Configuration ==

|| '''Main''' || Check to make this surface configuration the currently displayed one. ||
|| '''Inflated''' ||
|| '''White''' ||
|| '''Pial''' ||
|| '''Original''' ||

== Overlay Layer ==

|| '''Overlay Layer 1-9''' || Check to make this overlay layer the currently displayed one. ||

== Label Style ==

|| '''Filled''' || Check to show labels as filled areas. ||
|| '''Outline''' || Check to show labels as outlined areas. ||

== Tools ==

|| '''Save Point''' || Saves the current cursor so that TkSurfer or TkMedit can use its Goto Saved Point function to go to that point. ||
|| '''Goto Saved Point''' || Sets the cursor to the one last saved in TkSurfer or TkMedit for this subject. ||
|| '''Send to Subject...''' || Saves the current cursor in a different subject's cursor file, so they can use '''Goto Saved Point''' to go to the same location. ||
|| '''Select Vertex...''' || Sets the cursor to a vertex by number. You may need to rotate the surface to see the new point. ||
|| '''Run Script...''' || Executes a tcl script. ||
|| '''Labels''' || Shows a submenu of label tools. ||
|| '''Cut''' || Shows a submenu of surface cutting tools. ||
|| '''Time Course''' || Shows a submenu of time course tools. ||
|| '''Fill''' || Shows a submenu of label filling tools. ||
|| '''Surface''' || Shows a submenu of surface geography related tools. ||
|| '''Group''' || Shows a submeny of group analysis related tools. ||
|| '''Save RGB As...''' || Saves the contents of the Display window to an RGB file. ||
|| '''Save TIFF As...''' || Saves the contents of the Display window to an TIFF file. ||
|| '''Make Frame''' || Generates a movie frame in the subject's {{{rgb}}} directory. ||

=== Labels ===

|| '''New Label from Marked Vertices''' || Creates a new label containing the vertices currently marked.  ||
|| '''Mark Selected Label''' || Marks all vertices in the currently selected label. ||
|| '''Delete Selected Label''' || Deletes the currently selected label. ||
|| '''Delete All Labels''' || Deletes all labels. ||
|| '''Copy Label Statistics to Overlay...''' || Creates a new overlay layer, copying in the stat values from the current label. ||
|| '''Erode Selected Label''' || Enlarges the current label. ||
|| '''Dilate Selected Label''' || Shrinks the current label. ||

=== Cut ===

|| '''Cut Line''' || Calculates a line between marked vertices and cuts the vertices in that line. ||
|| '''Cut Closed Line''' || Same as above, but closes the line between the first and last marked vertex. ||
|| '''Cut Plane''' || Requires exactly four vertices to be marked. Cuts the surface but not in the plane defined by the four vertices. ||
|| '''Fill Uncut Area''' || Requires one marked vertex and two noncontiguous surface areas. Cuts the area that the marked vertex is not in. ||
|| '''Clear Cuts''' || Removes all cut vertex, restoring the surface to whole. ||
|| '''Dilate Cuts''' || Enlarge cut areas. ||

=== Time Course ===

|| '''Graph Marked Vertices Avg''' || Graphs the average of marked vertices in the time course. ||
|| '''Graph Label Avg''' || Graphs the average of a label in the time course. ||
|| '''Write Summary of Marked Vertices...''' || Writes a text file containing summary of time course info for the marked vertices. ||
|| '''Write Summary of Label...''' || Writes a text file containing summary of time course info for the vertices in the current label. ||
|| '''Save Graph to Postscript File''' || Saves the contents of the time course graph to a Postscript file. ||
|| '''Save Graphs of Series to Postscript File''' || Saves a series of files of time course graphs, one for each vertex in the current path or marked vertices. ||

=== Fill ===

|| '''Make Path''' || Make a path between marked vertices. ||
|| '''Delete Selected Path''' || Deletes the selected path. ||
|| '''Custom Fill...''' || Opens the Custom Fill dialog box. ||
|| '''Fill Stats''' || Marks vertices based on the overlay values surrounding the cursor. ||
|| '''Fill Curvature''' || Marks the region around each selected vertex that has a similar curvature to that of the selected curvature. ||

=== Surface ===

|| '''Smooth Curvature...''' || Smooths the curvature on the surface. ||
|| '''Clear Curvature''' || Sets the curvature value at each vertex to 0. ||
|| '''Smooth Overlay...''' || Iteratively smooths scalar for a user-selected number of iterations. Equivalent to convolving with a surface-based gaussian. ||
|| '''Inflate....''' || Applies the inflation force for a user-specified number of iterations, to smooth the surface. ||
|| '''Swap Surface Fields...''' || Intended for use by those who know the internal data structure of the surface. Opens a dialog box allowing you to specify two surface vertex fields to swap. ||
|| '''Write Decimation...''' || Write decimation values at each vertex to a value file. ||
|| '''Write Dipoles...''' || Write dipole values at each vertex to a value file. ||
|| '''Average Background Midpoint''' || In the curvature colorscale, sets the point at which red transitions to green to the mean curvature across the whole surface, making the data more interpretable. ||
|| '''Mask Values to Label...''' || Loads a label file and sets all overlay values not in the surface to 0. ||