Menus

Contents

Menus

File

Load Main Volume...	Loads a volume as the Main volume.
Save Main Volume	Saves the Main volume, overwriting the original data.
Save Main Volume AS...	Saves the Main volume into a new file, leaving the original data untouched.
Aux Volume	Submenu with volume commands for the Aux volume.

Load Main Surface...	Loads a surface overlay (e.g. orig.?h, white.?h, pial.?h) as the Main surface, looking for other configurations and loading them available.
Load Surface Configuration	Loads an alternate (Original or Pial) surface configuration for the Main surface.
Load Annotation	Loads a surface annotion (.annot file) created in TkSurfer into the current Main surface.
Unload Surface	Removes the Main surface and all configurations.
Write Surface Values...	Writes the current values associated with each Main surface vertex to a surface value file.
Aux Surface	Submenu with surface commands for the Aux surface.

Load Overlay Data...	Reads in coregistered functional data for 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.

New Segmentation...	Creates a new, empty segmentation, using the Main anatomical volume as a template, as the Main segmentation.
Load Segmentation...	Loads the Main segmentation, requiring volume data and a color lookup table file.
Import Surface Annotation as Segmentation...	Imports a surface annotion (.annot file) created in TkSurfer as the Main segmentation volume.
Save Segmentation	Saves the segmentation in its original file location.
Save Segmentation As...	Saves the segmentation in a new file or directory.
Save Changed Values	Saves a segmentation volume consisting of only the segmentation values that have been changed during this session.
Aux Segmentation	Sebmenu with commands for the Aux segmentation.

Transforms	Submenu with commands for loading volume display transforms.
Label	Submenu with commands for loading and saving labels.
GCA	Submenu with commands for loading and saving GCA volumes.
Head Points	Submenu with commands for loading and saving head points data.
DTI	Submenu with commands for loading DTI data.
Save Control Points	Save the control points file (for saving the file with removed points).

Quit

Quit.

Load Surface Configuration

Original Vertices	Load the Original vertex set for an exisiting surface
Pial Vertices	Load the Pial vertex set for an exisiting surface

Transforms

Load Transform for Main Volume...	Load an LTA or XFM file display transform for the Main anatomical volume.
Load Transform for Aux Volume...	Load an LTA or XFM file display transform for the Aux anatomical volume.
Unload Transform for Main Volume	Unload an LTA or XFM file display transform from the Main anatomical volume.
Unload Transform for Aux Volume	Unload an LTA or XFM file display transform from the Aux anatomical volume.

Label

Load Label...	Load a label file and add it to the current selection.
Save Label As...	Save the current selection as a label file.

GCA

Load GCA	Load GCA volumes.
Save GCA	Save GCA volumes.
Unload GCA	Unload GCA volumes.

Head Points

Load Head Points...	Load a list of head points.
Save Head Point Transform	Save a modified head point transform (overwrites existing).
Save Head Points	Save list of head points.

DTI

Load DTI Volumes...

Load DTI volumes.

Edit

Undo Last Edit

Undoes the last volume or segmentation edit.

Take Snapshot of Volume	Makes a copy of the current Main volume in memory.
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.

View

View Configurations

Shows a submenu of view configurations: Single View, Multiple Views, or Mosaic. See TkMeditViewingArea.

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 dialog boxes that allow viewing characteristics to be configured.
Anatomical Sampling	Change the anatomical sampling method for the Main or Aux anatomical volumes. See TkMeditAnatomicalVolumes
Anatomical Resampling	Change the way that the Main and Aux volume is resampled into coordinate space. See TkMeditAnatomicalVolumes

Anatomical Volume	Check to display the anatomical volume.
Main Volume, Aux Volume	Toggle between showing the Main or 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.
Functional Scale Color Bar	Check to show the color scale bar for the overlay.
Mask to Functional Overlay	Check to mask the anatomical volume to valid functional overlay space.
Mask Functional Overlay to Aux Volume	Only displays functional values that register to non-zero values in the Aux volume.
Show Histogram Percent Change	Check to show the window displaying changes in VLI label volumes.
Segmentation Overlay	Check to show the Main segmentation overlay.
Aux Segementation Overlay	Check to show the Aux 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.
DTI Overlay	Check to show the DTI overlay.
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.
Edited Voxels	Check to show the edited and undoable voxels in the Undo Volume.

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.

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, Line), View Configuration (Single, Multiple, Mosaic), Surface Display (Main, Original, Pial), Current Volume (Main, Aux), Segmentation, Functional Overlay, Functional Color Bar
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, Linked Cursors
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

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.
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.
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 the Main segmentation that the voxel is a part of.
Aux Segmentation Label	Check to show the name of the ROI in the Aux 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.
Surface Distance	Check to show the distance from the last cursor location to the present mouse or cursor location. (Used in setting surface distance values.)
Line Length	The length of the current line.

Configure...

Brightness / Contrast...	Opens a dialog box in which you can set the brightness, contrast, and min and max values 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. See TkMeditSurfaces
Functional Overlay...	Opens a dialog box in which you can change various characteristics of the functional overlay. See TkMeditFunctionalVolumes
Time Course Graph...	Opens a dialog box in which you can change various characteristics of the time course graph. See TkMeditFunctionalVolumes
Segmentation Display...	Opens a dialog box in which you can change the overlay opacity of the segmentation display.
DTI Display...	Opens a dialog box in which you can change the overlay opacity of the DTI display.

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.
Line	Changes the current tool to the Line Tool.

Configure Brush Info...	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.
Configure Flood Select...	Opens a dialog box in which you can change the parameters for the flood action of the Select Voxels 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.
Goto Center of Selection	Sets the cursor to the center of the selection.

Add Line to Selection	If a line is drawn, selects the voxels in the line.
Write Line to Label...	If a line is drawn, makes a new label out of the voxels in the line.
Label Writer Helper...	Shows the Label Writer Helper dialog box.

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.
Save TIFF...	Saves the contents of the Display Window to an TIFF file.
Save TIFF Series...	Opens a dialog box in which you can tell TkMedit to automatically scroll through a series of slices and save their images to TIFF files.

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.
Smart Cut	A tool for setting large sections of the Main anatomical volume to 0. See the Working With Data section for details.

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.

Show Nearest Main Surface Edge	Sets the cursor to the point of the nearest interpolated vertex on the Main surface configuration.
Show Nearest Original Surface Edge	Sets the cursor to the point of the nearest interpolated vertex on the Original surface configuration.
Show Nearest Pial Surface Edge	Sets the cursor to the point of the nearest interpolated 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.

Set Vertex Distance at Cursor	Sets the value in the Surface Distance information field for the closest vertex in the Main surface.
Set MRI Value in Surface	Submenu which lets you set the value in the surface for the Main, Original, or Pieal vertex sets to the current MRI value.
Average Vertex Positions...	Opens a dialog in which you can execute a command to average surface vertex positions in the Main surface.

fMRI

Select Contiguous 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.
Select Contiguous Voxels by Threshold	Selects contiguous voxels to the cursor whose corresponding functional values are greater than or equal to the minimum functional threshold value.
Select Functional Voxel	Selects an entire functional voxel.
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.

Segmentation

Recompute Segmentation	Recomputes the Main segmentation using the Main anatomical volume and the GCA volume.
Select Main Segmentation Label At Cursor	Selects all the anatomical voxels in the segmentation label in the Main segmentation volume under the cursor.
Select Aux Segmentation Label At Cursor	Selects all the anatomical voxels in the segmentation label in the Aux segmentation volume under the cursor.
Verbos GCA Display	If a GCA volume is loaded, this will print detailed information about the point clicked.

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.