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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)