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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.

TkSurferGuide/TkSurferReference/TkSurferMenus (last edited 2008-04-29 11:45:56 by localhost)