Attributes Menu


Area Colors  submenu for dealing with area colors.

Areal Estimation  submenu for dealing with areal estimation

Connectivity  displays a dialog for accessing connectivity functions.

Lat/Long  submenu for dealing with latitude/longitude.

Metrics  submenu for dealing with metrics.

Paint  submenu for dealing with node paints.

Palette  submenu for color palettes.

Parameters  submenu for parameters file.

Probabilistic Atlas  submenu for dealing with probabilistic atlases

Surface Shape  submenu for dealing with surface shape.

Vectors submenu for dealing with surface vectors.

Vocabulary  submenu for dealing with Vocabulary Files.


Generate Deformation Field
  launches a dialog for generating a deformation field.  The surfaces specified MUST BE spherical surfaces.

Generate Topography From Borders and Paint  Launches a dialog for generating visual topography.

Copy Current Coloring to RGB Paint  Copies the current node colors to a new columns in the RGB Paint file.  

Copy Current Coloring to RGB Volume
Launches a dialog for for creating an RGB Volume whose voxels are RGB values of a surface "placed" in the volume.

Map Volumes to Surfaces - Map volume data files (functional or paint) to a surface.

Area Colors Submenu


Edit  Displays a dialog for adding, editing, and deleting area colors.

Areal Estimation Submenu

Generate Areal Estimation Map  launches a dialog for creating an areal estimation map.

Lat/Long Submenu

Generate Lat/Long on Spherical Surface  Launches a dialog that enables the user to choose the Lat/Long file column and its name which will contain the latitude/longitude coordinates of all nodes on the spherical surface in the main window.  This assumes that the default view of the sphere (produced by pressing the "R" button in the toolbar) is a dorsal view.  Positive latitiude is along the lateral axis and negative latitude is along the medial axis.

Metrics Submenu

Clustering and Smoothing  Launches a dialog for clustering and smoothing metric data.

Compute Average and Sample Standard Deviation  The average and sample standard deviation (when compute the standard deviation the true mean is assumed to be unknown so division by "N-1" is used when computing the standard deviation) are computed for each node's metric values.  The results are placed in metric columns named Average and Deviation.  If the metrics columns named Average or Deviation exist, they are updated but their values are not included in the computations.

Mathematical Operations
  Displays a dialog for performing mathematical operations on columns in a metric file.

Convert Metric Column to Functional Volume Launches a dialog for creating a volume whose voxels are metric values of a surface "placed" in the volume.

Convert Metrics to RGB Paint  Displays a dialog that allows three metric columns to be mapped to the red, green, and blue components of a metric file.  This is useful for displaying three metrics simultaneously.


Paint Submenu

Assign Nodes Within Displayed Borders  Any nodes inside a displayed border are assigned the name of the border.  Area colors are not updated and must be updated by the user.  This operation is typically run on a flat surface.

Cleanup Paint Names  Removes unused paint names from the currently loaded paint file.

Convert Paint Column to Paint Volume Launches a dialog for creating a volume whose voxels are paint indices of a surface "placed" in the volume.

Edit Paint Names  Launches a dialog for editing the names contained in the paint file.

Generate Color for Paints Without Colors  If there are any paint names that do not have area colors with names that match exactly, a new random color is created for the paint name and added to the area color file.

Palette


Edit  Launches a dialog for editing color palettes.

Parameters


Edit Launches a dialog for editing the parameters file.

Probabilistic Atlas


Convert Threshold Coloring to Paint  Converts the currently selected threshold probabilistic overlay/underlay into a paint file column.

Study Metadata Submenu

Edit Collections  Launches a dialog for editing study collections

Edit Studies   Launches a dialog for editing studies.

Surface Shape Submenu

Clustering and Smoothing  Launches a dialog for clustering and smoothing surface shape data.

Mathematical Operations  Displays a dialog for performing mathematical operations on columns in the surface shape file.

Compute Average and Sample Standard Deviation  The average and standard deviation (when compute the standard deviation the true mean is assumed to be unknown so division by "N-1" is used when computing the standard deviation) are computed for each node's metric values.  The results are placed in metric columns named Average and Deviation.  If the metrics columns named Average or Deviation exist, they are updated but their values are not included in the computations.

Convert Surface Shape Column to Functional Volume Launches a dialog for creating a volume whose voxels are surface shape values of a surface "placed" in the volume.



Vectors Submenu


Create Vectors From Surface Subtraction - Create vectors between corresponding nodes in two surface currently loaded in Caret.

Create Vectors from Surface Normals - Create vectors using the normal vectors from the main window surface.



Vocabulary Submenu


Edit   Launches a dialog for editing the contents of a vocabulary file.

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