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.