Surface To Volume Dialog

The surface to volume conversion is performed by testing for intersection between each triangle in the surface and the volume's voxels that are within a bounding box of the triangle.  Since the surface is "infinitely thin", multiple iterations of intersecting the surface with the volume are performed by shrinking or expanding the surface by moving nodes along their surface normals in order to approximate the thickness of the cortex.  The process starts by shrinking the surface by "Inner Boundary".  The process then alternates intersecting the surface with the volume and moving the surface nodes along their normals by "Intersection Step" until the surface nodes have moved along their normals to "Outer Boundary". 

It is a Caret standard that the surface and volume are in LPI (left, posterior, inferior) origination.  After the volume is created, it can be saved using the Save Data File dialog accessible from the File menu.

Surface Selection

Fiducial Surface - If there is more than one fiducial surface loaded, the user should select the desired fiducial surface for the surface to volume conversion.

Inner Boundary - The surface is shrunk by this amount prior to the first iteration of intersecting the surface with the volume.

Outer Boundary - The iterations of intersecting the surface with the volume's voxels continue until the surface has expanded by this amount.

Intersection Step - This value determines how much the surface is expanded by after each iteration of surface and volume intersection.

Translate - This parameter is used to translate the surface so that it is in the same coordinate system as the volume.  Volume files such as AFNI, SPM, or WU-NIL contain information that either directly or indirectly identifies the location of the Anterior Commissure.  Typically, if the surface's origin is at the Anterior Commissure, the translation are set to zero.

Volume Selection

Space - If the surface has been derived from a volume that is a "standard space", the space can be selected which provoide the necessary volume parameters (dimension, voxel size, and origin).  If the surface was not derived from a standard space, NON-STANDARD should be selected for the Space and the volume parameters will need to be set by the user.

Note that WU 711-2B 222 and WU 7112B 333 spaces receive special processing.  With these spaces the surface to volume intersection is performed with a 1mm size voxel volume.  After the surface to volume intersections are completed, the volume is downsampled to the appropriate voxel size.  Since each 222 or 333 voxel is the equivalent size of 8 or 27 111 voxels, the 222 or 333 voxels are only set if a majority of the corresponding 111 voxels are non-zero.  It is therefore important that a minimum surface thickness of 2 or 3 millimeters is used.  Otherwise, insufficient voxels will be set and the "majority test" will fail during resampling.

Dimension - Enter the number of voxels in each axis.

Voxel Size - Enter the size of the voxel in each axis.

Volume Origin - Specify the coordinate (in millimeters) of the most left, anterior, inferior voxel in the volume as an offset from the anterior commissure.  If you know the voxel indices of the Anterior Commissure, the "Enter AC to Determine Origin" button can be selected to enter the AC and the origin will then be determined.

Enter AC to Determine Origin - If the voxel indices of the Anterior Commissure are known, pressing the button displays a dialog that allows entering of the AC voxel indices.  These voxel indices along with the Voxel Size are used to set the origin.

Get Parameters Using a Volume File - Pressing the button displays a file dialog for selecting a volume file.  The volume file's dimension, voxel size, and origin are placed into the dialog.

Paint Section

This section is present only if converting a paint column to volume file.  It allows selection of the paint column that is to be used for converting to a volume.