Layers Menu


Borders  Submenu for borders

Cells  Submenu for cells

Contours  Submenu for contours

Contour Cells  Submenu for contour cells

Foci   Submenu for foci


Borders Submenu

Convert Volume Borders to Fiducial Borders  Copies volume borders into fiducial borders.

Convert Volume Borders to Fiducial Cells  Copies volume borders into fiducial cells.  Needed border colors will be copied to the cell colors.

Convert Displayed Borders to VTK Model  Converts all displayed surface borders into a VTK model that is displayed using the Display Control's Models page.

Create Average Borders  Displays a dialog for creating an average border file from a set of border files with identically named borders.

Create Borders From Paint Regions  Creates borders around paint regions for a selected paint file column.  The algorithm will probably work best on a surface with a closed topology.

Create Cartesian Flat Grid Borders  Creates border in a grid pattern over the flat surface in the main window.  Typically placed over a flat surface for examining the effects of registration.

Create Cartesian Flat Analysis Grid Borders  Creates border in a grid pattern over the flat surface in the main window and used for third party analysis program.

Create Interpolated Borders  Launches a dialog that allows the user to create new borders by interpolating between two selected  borders.

Create Lat/Lon Spherical Borders  Creates latitude/longitude borders on the spherical surface in the main window.

Draw Border  Displays a dialog for drawing borders.

Draw Border Update  Allows redrawing of a segment of an existing border.  To use, select this menu item, make selections on the Draw Border  Update Dialog, move the mouse to the location in the border where the new region should begin, hold down the left mouse button and draw the new segment stopping near the end of the region that is being replaced, release the left mouse button, and lastly hold down the SHIFT key and click the left mouse button. 

Duplicate Border By Name  Launches a dialog that allows the user to make a copy of a border with a new name.

Edit Border Attributes  Displays a dialog that displays the sampling, variance, topography, and areal uncertainty for each unique border name.  The border names can also be changed and borders can be deleted by name by unchecking corresponding the Keep checkbox.

Edit Border Colors  Displays a dialog for adding, creating, and deleting border colors.

Clear Border Highlighting  Disable any highlighting of borders.  Highlighted borders are displayed in "double thickness".  Highlighted borders are created using the Border Color Key dialog and clicking on a color swatch.

Move Border Point With Mouse  Places the mouse in a mode that allows border points to be removed by pressing and holding down the mouse over a border point and moving the border point.

Rename Borders With Mouse  Places the mouse in a mode in such a way that clicking on a border pops up a dialog that allows renaming the border.

Reverse Borders With Mouse  Reverses the orientation each border that is clicked with the mouse.

Orient Displayed Borders Clockwise  Orients the borders on a flat surface clockwise.

Resample Displayed Borders  Resamples all displayed border to a specified value.

Reverse Displayed Borders
 Reverse the orientation of all displayed borders.

Project Borders   Project the borders from the surface in the main window to all other surfaces.  Any existing borders on other surfaces are destroyed.

Delete All Borders  Deletes all borders.

Delete Borders By Name  Launches a dialog for selecting the names of borders for deletion.

Delete Border Point With Mouse  Delete each border point that is clicked with the mouse.

Delete Border With Mouse  Delete each border that is clicked with the mouse.

Delete Border Points Outside Surface  Delete all border points that are outside the flat surface in the main window.



Cells Submenu

Add Cells With Mouse  Launches a dialog for entering cell naming and color information and then  allows entering cells by clicking on the surface.

Cell Report  Launches a dialog that allows the user to choose the cell attributes for the cell report that is displayed in a table.  The table allows saving of the cell report to a text file.

Convert Cell Density to Metric  Converts cells to a metric file that indicates the cell density over regions of a flat surface.

Convert Displayed Cells to VTK Model  Converts all displayed surface cells into a VTK model that is displayed using the Display Control's Models page.

Edit Cell Attributes  Allows cells to be deleted and edited by name.

Edit Cell Colors  Add, create, and delete cell colors.

Project Fiducial Cells  Project cells from the fiducial surface to all other surfaces.

Delete All Cells  Delete all cells.

Delete Cells With Mouse  Delete each cell that is clicked with the mouse.


Contours Submenu


Create New Contour Set  Enable contours so that they can be drawn.

Contour Information  Show a dialog containing information about the contours loaded in Caret.

Set Contour Scale  Launches a dialog for setting the scale of contours.  

Select Contour Sections  Launches a dialog for controlling which contour sections are displayed.

Set Contour Section Spacing  Launches a dialog for entering the spacing between sections.

Draw Contours  Launches a dialog for drawing contours.

Apply Current View  Applys the current transformation to the contours.

Align Contours  Launches a dialog for aligning contours.

Merge Contours  Places the mouse in a mode that allows contours to be merged.

Move Contour Point With Mouse  Places the mouse in a mode so that contour points can be moved.

Resample All Contours  User enters a value for the new spacing between contour points.

Reverse Contour With Mouse  Places the mouse in a mode so if a contour is clicked with the mouse, the order of the points in the contour is reversed.

Clean Up Contours  Removes consecutive, duplicate points from contours.  All contours with less than 3 points are deleted.

Delete All Contours  Deletes all contours.

Delete Contour With Mouse  Places the mouse in a mode so that contours are deleted when the mouse is clicked on a contour.

Delete Contour Point With Mouse  Places the mouse in a mode so that contour points are deleted when the mouse is clicked on a contour point.

Reconstruct Into Surface  Reconstructs the current contours into a surface.


Contour Cells Submenu


Add Contour Cells  Launches a dialog for entering contour cells.

Delete All Contour Cells  Deletes all contour cells.

Delete Contour Cells With Mouse  Places the mouse in a mode so that contour cells are deleted when the mouse is clicked on a contour cell.

Edit Contour Cell Colors   Launches a dialog for editing contour cell colors.

Move Contour Cells With Mouse  Places the mouse in a mode that allows contour cells to be moved by pressing the mouse, dragging the contour cell to a new location, and releasing the mouse.

Foci Submenu

Assign Class to Displayed Foci  Allows the user to enter the name of a class that is assigned to all displayed foci.  If a corresponding color does not exist, the user is prompted to set the color.

Attribute Assignment  Assign attributes such as Area and Geography using surfaces and node data files.  For example, assign Brodmann areas from the paint file to foci Area attribute.

Convert Foci Density to Metric  Converts foci to a metric file that indicates the cell density over regions of a flat surface.

Convert Foci Density to Functional Volume  Converts foci to a functional volume where the voxel is the number of foci per millimeter.

Convert Uncertainty Limits to RGB Paint  Create an RGB Paint file where the node coloring reflects the proximity of foci using the fiducial surface.

Convert Displayed Foci to VTK Model  Converts all displayed surface cells into a VTK model that is displayed using the Display Control's Models page.

Clear Foci Highlighting  Removes any highlighting of foci.  Foci are typically highlighted using the Foci Color Key by clicking the mouse on the foci's color.

Foci Report  Launches a dialog that allows the user to choose the foci attributes for the foci report that is displayed in a table.  The table allows saving of the foci report to a text file.

Foci Attribute Report  Launces a dialog that allows the user to choose an attribute whose values are displayed in a table.  The table allows saving of the report to a text file.

Map Stereotaxic Focus  Enter Stereotaxic coordinates of foci and display on all surfaces.

Edit Foci Colors   Add, create, and delete foci colors.

Delete Foci Colors Not Matching Foci  Remove all foci colors which do not match the start of any of the loaded foci projection names.

Project Fiducial Foci  Project foci from the fiducial surface to all other surfaces.

Project Foci to PALS Atlas  This option is only enabled if a PALS compatible surface is loaded (surface has 73730 nodes).  With this projection method, foci are mapped to the PALS left or right hemisphere in the same stereotaxic space as the focus.

Project Foci to Volume  Launches a dialog for choosing left and right surfaces that are used for determing the coordinates of foci in the volume.  The left and right surfaces should be in the same stereotaxic space as the volume on which the foci will be viewed so that the volume coordinates of the foci are correct.

Delete All Foci  Delete all foci.

Delete Foci Not Displayed due to Display Control Selections
  Deletes foci that are not displayed based upon the Display Control's Foci Selections.  If there is a surface in the Main Window, you may also choose to delete foci that are not displayed on the surface (foci associated with the other hemisphere).

Delete Focus Using Mouse  Delete each focus that is clicked on with the mouse.

Update Focus' PubMed ID if Focus Name Matches Study Name  Compare the name of each focus to the name of each Study in the Study Metadata File Study.  If the focus' name matches the name of a study, set the the focus' study metadata link to the PubMed ID contained in the study.

Update Focus' Class Name with Table/Fig/Page Short Names   If the focus is linked to a table, figure, or page reference, replace the class name with the table's subheader short name, figure panel task description, or page reference subheader short name.
Update Focus' Class Name With Table Subheader Short Names  If the focus is linked to a table's subheader, set the focus' class name to the short name from the table's subheader.

Move Foci Study Info to Study Metadata File   Moves StudyInfo from the Foci Projection File into the Study Metadata File.  All links from foci to the Study Metadata are updated.  After this operation is performed, the Foci Projection and Study Metadata files need to be saved.