Surface Menu

Align Surface(s) to Standard Orientation - Launches a dialog for aligning a flat map and sphere to the standard orientation.

Automatic Rotation  Launches a dialog for rotating the surface in the main window.

Convert Main Window Surface to Segmentation Volume
  Launches a dialog for choosing the size of the segmentation volume derived from the main window surface.

Copy Main Window Surface to New Surface  Makes a copy of the surface in the main window.

Create Average Coordinate File
 Launches a dialog for creating average coordinate files.

Cuts Submenu

Deformation Submenu

Edit Submenu

Flatten Full or Partial Hemisphere  Launches a dialog for flattening a full or partial hemisphere.

Geometry Submenu

Identity Submenu

Information  Displays information about the surface in the main window and allows setting the "active" fiducial surface.

Interpolate Surfaces  Interpolate between two surfaces.

Measurements Submenu

Morphing Submenu

Normals Submenu

Project to Plane Launches a dialog for projecting coordinates to a plane. 

Region of Interest Operations  Launches the Surface Region of Interest Dialog.

Sections Submenu

Simplify Surface (Fewer Polygons)  Reduce the number of polygons (and nodes) in a surface.  This may be useful if a surface generated by another program has too many polygons/nodes, making the surface slow to operate upon.

Topoogy Submenu

Transform Submenu

View Submenu



Cuts Submenu


Show Cuts  Toggles the display of cuts.

Apply All Cuts  Applies all cuts to the surface in the main window.

Delete Cut With Mouse  Places the mouse in a mode so that a cut is deleted when it is clicked with the mouse.

Delete All Cuts  Deletes all cuts.

Draw Cuts  Launches a dialog for drawing cuts.

Deformation Submenu


Apply Deformation Map  Launches a dialog for applying a deformation map file to a Caret data file.

Run Flat Surface Deformation  Launches a dialog for deforming one flat surface to another.

Run Spherical Surface Deformation
 Launches a dialog for deforming one spherical surface to another.

The Deformation algorithms are described at surfac-based registration.

Edit Submenu


For best results, on the Display Control Surface Miscellaneous panel, set the Drawing Mode to Nodes and Links.  Adding and moving of nodes assumes that flat surfaces are displayed.

Add Node  In this mode, each time the mouse is clicked, a node is added to the surface at the location of the mouse click.  For all other loaded surfaces, the new node is placed at the origin.  This option is enabled when the surface is drawn using a mode the shows the surface nodes.


Add Tile  In this mode a new tile (triangle) is added.  To add the tile, click on three nodes in succession.  Each time a node is clicked on, it will turn red.  When three nodes have been clicked on, a tile will be added and any of the clicked on nodes will return to their normal color.  Tiles should be created in counter-clockwise orientation.  This option is enabled when the surface is drawn using a mode the shows the surface nodes.

Delete Link  Click on a link which actually deletes the two tiles that form the link (for an interior link) or the tile that forms the link (for an edge link).

Disconnect Node  Click on a node to delete all tiles that are attached to the node.  This option is enabled when the surface is drawn using a mode the shows the surface nodes.


Move Node  Place the mouse over a node, and, while holding down the left mouse button, drag the node to its new location and release the left mouse button.  This option is enabled when the surface is drawn using a mode the shows the surface nodes.


Geometry Submenu

Compress Front Face  Compresses a spherical surface.

Compress Sphere Medial Wall  Compresses a spherical surface so that the nodes on the sphere are "pulled" towards the positive Z axis facing the user.  The surface's type then becomes Compressed Medial Wall.

Convert to Sphere  Converts the main window surface into a sphere.

Convert Ellipsoid to Sphere  Converts the ellipsoidal surface in the main window into a sphere.

Generate Inflated and Ellipsoid From Fiducial  Uses the active fiducial surface to generate both inflated and ellipsoidal surfaces.   If the surface has a large number of nodes, the inflated surfaces may not be sufficiently inflated.  The iterations scale may be used to increase the number of iterations during the inflation process.  If the surface has 150,000 nodes, try an iterations scale of 2.5.

Expand or Shrink Surface
 Expand or shrink a surface by moving its nodes along their normal vectors by a specified amount.  Use a negative value to shrink the surface or a positive value to expand the surface.  This may be useful for approximating a gray/white boundary or gray/CSF boundary surface.

Inflate Surface  Launches a dialog for inflating the surface in the main window.

Inflate Surface And Smooth Fingers  Launches a dialog for inflating a surface and smoothing "fingers".

Project Sphere to Flat  Projects the spherical surface in the main window to a flat surface.

Project Sphere to Flat Through Hole  Projects the sphere in the main window to a flat surface.  Prior to projecting flat, the sphere is oriented so that the nodes labels "CUT.FACE" or "MEDIAL.WALL" are oriented to the negative Z-Axis facing away from the user.

Scale Sphere to Fiducial Surface Area  Scale a spherical surface so that its surface area matches that of the active fiducial surface.

Smoothing  Launches a dialog for performing various types of smoothing on the main window surface.

Identity Submenu


Clear Node Identify Symbols - Removes all green symbols that were created when identifying nodes.

Identify Node By Number  -  Allows identification of a node by its number.

Identify Tile By Number - Allows identification of a tile's nodes by the tile number.


Measurements Submenu


Crossover Check  Performs a crossover check on the surface in the main window.

Generate Curvature  Launches a dialog for generating surface curvature.

Generate Distance: Surface A to Surface B  Find the three-dimensional distance between nodes in two different surfaces and place in a surface shape file column.

Generate Distortion  Launches a dialog for generating surface distortion.

The areal distortion for a tile:   log(tile-area  / reference-tile-area) / log(2.0)

The areal distortion for a node is the average of the distortions of each of the tiles used by the node.

The linear distortion for an edge (link):   (link-length / reference-link-length)

The linear distortion for a node is the average ofthe distortions of each of the links used by the node.

Generate Sulcal Depth  Launches a dialog for generating surface depth map.


Morphing Submenu


Morph Flat Surface
 Peforms morphing for a specified number of interations on the flat surface in the main window.

Morph Spherical Surface  Performs morphing for a specified number of iterations on the spherical surface in the main window.

Multiresolution Morphing Flat Surface
 Launches a dialog for flat multiresolution morphing.

Multiresolution Morphing Spherical Surface  Launches a dialog for spherical multiresolution morphing.


Normals Submenu


Flip Normals  Flips normals on the main window surface.

Generate Normals  Generate normals for the main window surface.


Sections Submenu


Clear All or Part of Section File  Launches a dialog for deleting some or all columns in a section file.

Resection  Launches a dialog for resectioning the main window surface.

Section Control  Launches a dialog for controlling the displayed sections.


Topology Submenu


Classify Nodes   Classifies nodes as edges or interior

Orient Tiles Consistently  Cleans up topology by ensuring that the surface triangles are consistently oriented.

Check For Islands  Determines the number of islands (extra pieces of disjoint connected surface) that are in the current surface.  Use Disconnect Islands to get rid of them.

Remove  Islands  Finds the largest piece (number of connected nodes) of connected surface and disconnects any other piece(s).

Remove Corner and Straggler Tiles  If a tile has a node that is unique to that tile (no other tile uses the node) that tile is "Corner" tile.  If a tile has two nodes that are unique to the tile (no other tile uses the two nodes) that tile is a "Straggler" tile.  Straggler tiles can cause problems during multiresolution morphing.

Set Topology Assigned to Surfaces  Launches a dialog for choosing the topology files assigned to surfaces.

Topology Error Report
 Displays a dialog which is used to examine a surface to determine if it is topologically correct.

Transform Submenu

Apply Current View  Applies the current view to the main window surface.

Apply SPM Inverse Transform  Applies an SPM inverse transformation to the main window surface.

Move Disconnected Nodes to Origin  Moves any disconnected nodes in the main window surface to the origin.

Scale  Scales the main window surface.

Translate  Translates the main window surface.

Translate - Subtract Params File AC  Translate the main window surface by subtracing the Parameters File Anterior Commissure.

Translate to Center of Mass  Translates the main window surface to its center of mass (average coordinate of its nodes).


View Submenu

Adjust View  Launches a dialog that allows the user to enter the translate, scale, and rotate for the surface in the main window.

Scale Surface To Fit Window  Scales the view of the surface so that it fills the window.  This can be useful after operations that modify the coordinates of the surface.

Save User View  Saves the current view to the user's preferences file.  A dialog allows a name to be entered for the view and the choice of saving any or all of the rotation, scaling, and translation.

Switch to User View  Changes the current view to a user's saved view (only if one or more has been created).





SPM Inverse Transform  Apply SPM inverse transforms to a fiducial coordinate file in Native space to an SPM Normalized Space.  In the dialog, select the currently loaded coordinate file that is to be transformed.  Select the normalized volume and then the three "iy" volumes.



Creating the inverse deformation files with SPM: