FsTutorial/TksurferReference - Free Surfer Wiki

Reference

1.0 Mouse commands

1.1 Mouse clicks

Button 1	Sets the cursor, drawing it in the new location, and marks the clicked vertex.
Button 2	Sets the cursor without drawing it in the new location and unmarks the clicked vertex.
Button 3	Clears marked vertices.

1.1 Mouse controls for zooming

Control+Button 1	Zooms in, doubling the zoom level
Control+Button 3	Zooms out, halving the zoom level

2.0 Menus

2.1 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.
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.

2.2 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

2.3 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.

2.4 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.

2.5 Label

Load Label...	Loads a label file.
Save Label	Saves changes to the label, overwriting the original file.
Save Label As...	Saves the label into a new file.

2.6 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.

2.7 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.

2.8 Edit

Undo	Undoes the cut.
Unmark All Vertices	Unmarks all vertices. Same as clicking with button 3 in the Graphics window.
Clear Label	Clears the vertices selected by loading a label.

2.9 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.
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.
Overlay	Check to display the current overlay layer.
Scale Bar	Check to display a scale bar in the window, showing the scale of 10 mm.
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.

2.10 Tool bars

Main

Check to make the Main toolbar visible. This toolbar contains the following controls: Cut Line, Cut Closed Line, Cut Plane, Cut Area, Clear Cuts, Save Point, Goto Saved Point, Restore Home View, Redraw View.

2.11 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 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 1-5	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.
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.
Parcellation	Check to show the name of the parcellation label of this vertex.

2.12 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.

2.13 Surface configuration

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

2.14 Overlay layer

Overlay Layer 1-5

Check to make this overlay layer the currently displayed one.

2.15 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.
Run Script...	Executes a tcl script.
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.
Cut Area	Requires one marked vertex and two incontiguous surface areas. Cuts the area that the marked vertex is not in.
Clear Cuts	Removes all cut vertex, restoring the surface to whole.
Send to Subject...	Same as Save Point, but allows you to enter a subject name explicitly.
Write Decimation...	Not functional, reserved for future upgrade.
Write Dipoles...	Writes a file containing the dipole values at each vertex.
Set Background Midpoint to Average	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.
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. Used for labeling anatomical regions.
Smooth...	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.
Clear Curvature	Sets the curvature value at each vertex to 0.
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.
Save Graph to Postscript File	Saves the contents of the time course graph to a Postscript file.
Save RGB As...	Saves the contents of the Display window to an RGB file.