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1. Menus
Index TableOfContents
1.1. 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. |
1.1.1. 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 |
1.1.2. Transforms
Load Transform for Main Volume... |
Load a display transform for the Main anatomical volume. |
Load Transform for Aux Volume... |
Load a display transform for the Aux anatomical volume. |
Unload Transform for Main Volume |
Unload a display transform from the Main anatomical volume. |
Unload Transform for Aux Volume |
Unload a display transform from the Aux anatomical volume. |
1.1.3. 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. |
1.1.4. GCA
Load GCA |
Load GCA volumes. |
Save GCA |
Save GCA volumes. |
Unload GCA |
Unload GCA volumes. |
1.1.5. 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. |
1.1.6. DTI
Load DTI Volumes... |
Load DTI volumes. |
1.1.7. 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. |
1.2. 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. |
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. |
1.2.1. 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. |
1.2.2. 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 |
1.2.3. 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.) |
1.2.4. 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. |
1.3. 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. |
1.3.1. 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. |
1.3.2. 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. |
1.3.3. 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. |
1.3.4. 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. |
1.3.5. 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. |