||Up to TkMeditGuide||Back to [[../TkMeditMouseCommands| TkMeditMouseCommands]]||Continue to [[../TkMeditScripting| TkMeditScripting]]|| = 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 [[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 dialog boxes that allow viewing characteristics to 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, 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 [[TkMeditGuide/TkMeditWorkWithData/TkMeditSurfaces| TkMeditSurfaces]]|| ||Functional Overlay...||Opens a dialog box in which you can change various characteristics of the functional overlay. See [[TkMeditGuide/TkMeditWorkWithData/TkMeditFunctionalVolumes| TkMeditFunctionalVolumes]]|| ||Time Course Graph...||Opens a dialog box in which you can change various characteristics of the time course graph. See [[TkMeditGuide/TkMeditWorkWithData/TkMeditFunctionalVolumes| 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.||