Differences between revisions 1 and 2
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
File '''File'''
Line 3: Line 3:
Load Main Volume...
 
|| 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.||
Line 6: Line 30:
Loads the Main volume from a directory of COR- files. ''File, 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||
Line 8: Line 34:
Load Aux Volume...
 
Line 11: Line 35:
Loads the Auxiliary volume from a directory of COR- files. ''File, 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.||
Line 13: Line 41:
Import Main Volume from File...
 
''File, 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.||
Line 16: Line 45:
Reads a specified file as the Main volume. ''File, GCA''
||Load GCA||Load GCA volumes.||
||Save GCA||Save GCA volumes.||
||Unload GCA||Unload GCA volumes.||
Line 18: Line 50:
Import Aux Volume from File...
 
''File, 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.||
Line 21: Line 55:
Reads a specified file as the Aux volume. ''File, DTI''
||Load DTI Volumes...||Load DTI volumes.||
Line 23: Line 58:
Load Transform for Main Volume...
 
Line 26: Line 59:
Loads an LTA or XFM file to use as the display transform for the Main volume. '''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.||
Line 28: Line 66:
Load Transform for Aux Volume...
 
Line 31: Line 67:
Loads an LTA or XFM file to use as the display transform for the Aux volume. '''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.||
Line 33: Line 94:
Unload Transform for Main Volume
 
''View, View Configurations''
Line 36: Line 96:
Removes the display transform for the Main volume. ||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.||
Line 38: Line 100:
Unload Transform for Aux Volume
 
''View, Tool Bars''
Line 41: Line 102:
Removes the display transform for the Main volume. ||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||
Line 43: Line 106:
Save Main Volume
 
''View, Information''
Line 46: Line 108:
Saves the Main volume in its original COR- file directory. ||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 48: Line 123:
Save Main Volume As...
 
''View, 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.||
Line 51: Line 132:
Saves the Main volume in a new directory. '''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.||
Line 53: Line 152:
Load Main Surface...
 
''Tools, 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.||
Line 56: Line 158:
Loads a surface overlay (e.g. orig.?h, white.?h, pial.?h), looking for other configurations and loading them available. ''Tools, 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.||
Line 58: Line 171:
Load Surface Configuration
 
''Tools, 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.||
Line 61: Line 182:
Loads an alternate (Original or Pial) surface configuration. ''Tools, 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.||
Line 63: Line 187:
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.
''Tools, 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.||

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.

File, 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

File, 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.

File, 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.

File, GCA

Load GCA

Load GCA volumes.

Save GCA

Save GCA volumes.

Unload GCA

Unload GCA volumes.

File, 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.

File, 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.

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.

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.

View, 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.

View, 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

View, 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.)

View, 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.

Tools, 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.

Tools, 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.

Tools, 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.

Tools, 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.

Tools, 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.

TkMeditGuide/TkMeditReference/TkMeditMenus (last edited 2008-04-29 11:46:14 by localhost)