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:
- Start matlab.
- Enter "spm" at the Matlab prompt to start SPM.
- Select "Pet and Spect".
- Press the "Defaults" button.
- Choose "Defaults for writing normalized" from the menu.
- Choose the bounding box: Template, Default, etc.
- Choose "1 1 1" for the voxel sizes.
- Press the "Normalize" button.
- Choose "Determine Parameters and Write Normalized" from the menu.
- Enter 1 for number of subjects and pres the return key.
- Choose the name of the ".img" file and press
Done.
- Choose the name of the ".img" file again and
press Done.
- Chose T1.img in the "Template Image" dialog and press Done.
- Choose "Bilinear" for the interpolate method. The process
will take about 10 minutes to complete.
- Press the "Toolboxes" button and select Deformations (note: there
are files in the Deformations toolbox that may need to be compiled.
If so, you will get a "ui callback" error.
- From the Deformations menu, select "Deformations from sn3d.mat".
- In the dialog that pops up, select the "<prefix>_sn3d.mat"
file. It may be necessary to use the previous directory
button to find it. Press the Done button and after several
minutes the process will finish.
- From the Deformations menu, select "Invert Deformations".
- Enter 1 and press return for "Number of Subjects".
- In the "Select deformation field 1" dialog, select the "y1",
"y2", and "y3" files and press the Done button.
- In the "Image to base inverse on" dialog, select your original
".img" file and press the Done button.
- The process will take about five minutes to complete. There
will now be six files (both .img and .hdr), "iy1", "iy2", and "iy1"
where the voxel in "iy1" is the X value the original voxel becomes when
deformed to the normalized volume. "iy2" and
"iy3" are the Y and Z locations.
- Press the Quit button to exit SPM.
- Type "quit" at the Matlab prompt to exit Matlab.