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Menus

TableOfContents

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 [:TkMeditGuide/TkMeditGeneralUsage/TkMeditViewingArea: 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 viewing characteristics that can be configured.

Anatomical Sampling

Change the anatomical sampling method for the Main or Aux anatomical volumes. See [:TkMeditGuide/TkMeditWorkingWithData/TkMeditAnatomicalVolumes: TkMeditAnatomicalVolumes]

Anatomical Resampling

Change the way that the Main and Aux volume is resampled into coordinate space. See [:TkMeditGuide/TkMeditWorkingWithData/TkMeditAnatomicalVolumes: TkMeditAnatomicalVolumes]


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.

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.

Show Histogram Percent Change

Check to show the window displaying changes in VLI label volumes.

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.

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), View Configuration (Single, Multiple, Mosaic), Surface Display (Main, Original, Pial), Current Volume (Main, Aux)

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 on

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.)

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.

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.

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.

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.

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.

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

Select Current Label

Selects all the anatomical voxels in the segmentation label under the cursor.

Recompute Segmentation

Recomputes the Main segmentation using the Main anatomical volume and the GCA volume.

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.