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
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.
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
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.
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.
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.