File
Load Main Volume...
Loads the Main volume from a directory of COR- files.
Load Aux Volume...
Loads the Auxiliary volume from a directory of COR- files.
Import Main Volume from File...
Reads a specified file as the Main volume.
Import Aux Volume from File...
Reads a specified file as the Aux volume.
Load Transform for Main Volume...
Loads an LTA or XFM file to use as the display transform for the Main volume.
Load Transform for Aux Volume...
Loads an LTA or XFM file to use as the display transform for the Aux volume.
Unload Transform for Main Volume
Removes the display transform for the Main volume.
Unload Transform for Aux Volume
Removes the display transform for the Main volume.
Save Main Volume
Saves the Main volume in its original COR- file directory.
Save Main Volume As...
Saves the Main volume in a new directory.
Load Main Surface...
Loads a surface overlay (e.g. orig.?h, white.?h, pial.?h), looking for other configurations and loading them available.
Load Surface Configuration
Loads an alternate (Original or Pial) surface configuration.
Unload Surface
Removes the surface and all configurations.
Load Overlay Data...
Reads in coregistered functional data for in-plane overlay.
Load Time Course Data...
Loads in coregistered functional data for graphing over multiple time points.
Save Overlay Registration
If registration has been enabled, this will save the registration to the register.dat file.
Load Segmentation...
Loads a segmentation, requiring a COR- file directory and a color lookup table file.
Save Segmentation
Saves the segmentation in its original COR- file directory.
Save Segmentation As....
Saves the segmentation in a new directory.
Load Label...
Reads in a cortical label file as the selection.
Save Label As...
Saves the selection as a cortical label file.
Load Head Points....
Loads a head points transform file and a list of MEG/EEG sensor points.
Save Head Point Transform
Saves an edited head points transform file.
Save Head Points
Saves head points.
Save Control Points
Saves control points to control.dat file. (Done automatically.)
Quit
Exits the program.
top Edit
Undo Last Edit
Undoes the last volume or segmentation edit.
Take Snapshot of Volume
Makes a copy of the current Main volume.
Restore Volume to Snapshot
Restores the Main volume to the saved copy.
Clear Label / Selection
Clears the current selection.
Clear Undo Volume
Clears the Undo Volume.
top View
View Configurations
Shows a submenu of view configurations.
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.
Anatomical Volume
Check to display the anatomical volume.
Main Volume
Toggle between showing the Main or Aux volume.
Aux Volume
Maximum Intensity Projection
Check to display the maximum intensity projection of the current volume, or the highest values in the current plane for each voxel.
Main Surface
Check to display the Main surface configuration.
Original Surface
Check to display the Original surface configuration.
Pial Surface
Check to display the Pial surface configuration.
Surface Vertices
Check to display the surface vertices on top of the surface overlay.
Interpolate Surface Vertices
Check to use interpolation to draw surface vertices. Uncheck to use projection.
Functional Overlay
Check to show the functional overlay volume.
Mask to Functional Overlay
Check to mask the anatomical volume to valid functional overlay space.
Segmentation Overlay
Check to show the segmentation overlay.
Segmentation Label Volume Count
Check to count the volume of a label in the segmentation when clicking with the left mouse button when the Edit Segmentation Tool is selected.
Selection / Label
Check to show the selection.
Head Points
Check to show the head points.
Control Points
Check to show the control points.
Cursor
Check to show the cursor.
Axes
Check to show the coordinate space axes.
Undoable Voxels
Check to show the undoable voxels in the Undo Volume.
top View Configurations
Single View
Displays one pane with a single orientation.
Multiple Orientations
Displays four panes, allowing all orientations to be viewed at the same time around the cursor.
Mosaic
Displays a 4x4 grid of different slices in the same orientation.
top Tool Bars
Main
Check to display the Main toolbar, which has the following controls: Tool Selector (Navigation, Select Voxels, Edit Voxels, Edit Segmentation, Edit Control Points), View Configuration (Single, Multiple, Mosaic), Surface Display (Main, Original, Pial), Current Volume (Main, Aux), Linked Cursors
Navigation
Check to display the Navigation toolbar, which has the following controls: Orientation (Coronal, Horizontal, Sagittal), Slice number, Zoom Out, Zoom In, Zoom Level, Save Point, Go To Saved Point
Reconstruction
Check to display the Reconstruction toolbar, which has the following controls: Brush shape (Circular, Square), 3D brush, Radius, Make Snapshot , Restore to Snapshot, TkTimer on
top Information
Volume Index Coordinates
Check to show the volume index coordinates (0..255).
Volume RAS Coordinates
Check to show the RAS coordinates. The origin is at the center of the volume.
Volume Scanner Coordinates
Check to show the scanner coordinates, usually the RAS coordinates.
Volume MNI Coordinates
Check to show the MNI Talairach coordinates. This was the old Talairach coordinate system, but has been replaced by a slightly modified version.
Volume Talairach Coordinates
Check to show the Talairach coordinates, determined by the talairach.xfm file for a subject. May not be available if this file is missing.
Volume Value
Check to show the value of the Main volume voxel.
Aux Volume Value
Check to show the value of the Aux volume voxel.
Functional Overlay Index Coordinates
Check to show the functional overlay volume index coordinates.
Functional Overlay RAS Coordinates
Check to show the functional overlay RAS coordinates. The origin is at the center of the functional volume.
Functional Overlay Value
Check to show the value of the functional overlay volume voxel.
Segmentation Label
Check to show the name of the ROI in a segmentation that the voxel is a part of.
Head Point Label
Check to show the name of the head point nearest the cursor or mouse.
top Configure...
Brightness / Contrast...
Opens a dialog box in which you can set the brightness and contrast of the Main and Aux volumes.
Cursor...
Opens a dialog box in which you can change the color and shape of the cursor.
Surface...
Opens a dialog box in which you can change the color and line width of each surface configuration.
Functional Overlay...
Opens a dialog box in which you can change various characteristics of the functional overlay.
Time Course Graph...
Opens a dialog box in which you can change various characteristics of the time course graph.
Segmentation Display...
Opens a dialog box in which you can change the overlay opacity of the segmentation display.
top Tools
Navigate
Changes the current tool to the Navigation Tool.
Select Voxels
Changes the current tool to the Select Voxels Tool.
Edit Voxels
Changes the current tool to the Edit Voxels Tool.
Edit Segmentation
Changes the current tool to the Edit Segmentation Tool.
Edit Control Points
Changes the current tool to the Edit Control Points Tool.
Configure Volume Shape...
Opens a dialog box in which you can change the size, shape, and depth of the brush.
Configure Volume Brush...
Opens a dialog box in which you can change the threshold and color values for the Edit Voxels Tool.
Configure Segmentation Brush...
Opens a dialog box in which you can change the color and fill settings for the Edit Segmentation Tool.
Save Point
Saves the current cursor so that TkSurfer can use its Go To Point function to go to that point.
Goto Saved Point
Sets the cursor to the one last saved in TkSurfer for this subject.
Goto Point...
Opens a dialog box in which you can enter specific numerical values in multiple coordinate systems and go to that point.
Volume
Opens a submenu of tools and commands for anatomical data.
Surface
Opens a submenu of tools and commands for surface data.
fMRI
Opens a submenu of tools and commands for to functional data.
Head Points
Opens a submenu of tools and commands for EEG/MEG head point data.
Save RGB...
Saves the contents of the Display Window to an RGB file.
Save RGB Series...
Opens a dialog box in which you can tell TkMedit to automatically scroll through a series of slices and save their images to RGB files.
top Volume
Threshold Volume...
A tool for changing all Main volume values above or below a specific value to a new value.
Flip Volume...
A tool for flipping the Main volume, creating a mirror image.
Rotate Volume...
A tool for rotating the Main volume any number of degrees around a main axis.
top Surface
Show Nearest Main Vertex
Sets the cursor to the point of the nearest vertex on the Main surface configuration.
Show Nearest Original Vertex
Sets the cursor to the point of the nearest vertex on the Original surface configuration.
Show Nearest Pial Vertex
Sets the cursor to the point of the nearest vertex on the Pial surface configuration.
Find Main Vertex...
Opens a dialog in which you can enter a vertex index on the Main surface. The cursor will be set to that index.
Find Original Vertex...
Opens a dialog in which you can enter a vertex index on the Original surface. The cursor will be set to that index.
Find Pial Vertex...
Opens a dialog in which you can enter a vertex index on the Pial surface. The cursor will be set to that index.
top fMRI
Select Continuous Voxels by Func Value
Selects contiguous voxels to the cursor whose corresponding functional values are greater than or equal to the functional value at the cursor.
Register Functional Overlay...
A tool for aligning (registering) the functional overlay data with the anatomical data.
Restore Overlay Registration
Restores the overlay registration to its original value.
Set Registration to Identity
Sets the overlay registration matrix to the identity matrix, removing all transformations.
Graph Current Selection
Graphs the average of all voxel values in the selection in the Time Course graph window.
Print Time Course Summary to File...
Creates a file containing a table version of the time course information for the current voxel or selection.
Save Time Course Graph to Postscript File...
Saves the contents of the Time Course graph window to a Postscript file suitable for printing or including in other documents.
top
Segmentation
Select Current Label
Selects all the anatomical voxels in the segmentation label under the cursor.
Graph Current Label Average
Graphs the average time course for all the anatomical voxels in the segmentation label under the cursor. Only works with a time course loaded. Head Points
Restore Head Points
Restores the head points registration to its original value.
Edit Current Head Point Label...
Edits the label of the head point closest to the cursor.
Register Head Points...
A tool for aligning the head point data with the anatomical data.