NA-MICNational Alliance for Medical Image Computing http://na-mic.org

Adding Orientation to itkImage

National Alliance for Medical Image Computing http://na-mic.org

Motivation

National Alliance for Medical Image Computing http://na-mic.org

Image Coordinate Systems

• Coordinate systems are an important part of any medical application.

• Medical scanners create regular, "rectangular" arrays of points and cells.

• The topology of the arrays is implicit in the representation.

• The geometric location of each point is also implicit.

National Alliance for Medical Image Computing http://na-mic.org

vtk and itk images

• vtk and itk store meta-information that can be used to convert between image coordinates (i-j-k) and world coordinates (x-y-z).

• Each image has an origin that is a 3-D (n-D for itk) vector. The origin (x-y-z) specifies the world coordinate of the first point in memory. The spacing specifies the distance between points along each axis.

• Using the spacing and origin, the transformation between i-j-k and x-y-z is a fast, simple computation.– x(yz) = origin + i(jk) * spacing;– i(jk) = (x(yz) - origin) / spacing;

National Alliance for Medical Image Computing http://na-mic.org

Requirement: Location + Orientation

space: right-anterior-superiorspace origin: (117.5,-93,119)space directions: (-0.859375,0,0) (0,0,-0.859375) (0,5,0) none

right

anterior

superior(RAS)

fast

medium

slow(image)

National Alliance for Medical Image Computing http://na-mic.org

Proposed extensions to itk::Image

• Add an itk::Matrix containing direction cosines• The i-j-k -> x-y-z transformation could include the

orientation in the computation.• Adding the matrix will not change the existing API.• Almost all index to point calculations are confined to

itk::Image.• The transformations in matrix form are:

– XYZ = To * Rc * Ss * IJKwhere To is a translate to the origin, Rc is the matrix of direction cosines and Ss is a scale matrix of spacings.

• There are performance considerations, so the implementation may cache some internal matrices and state.

National Alliance for Medical Image Computing http://na-mic.org

Next Steps

• Continue discussion on the Wiki– NAMIC Wiki:Community Coordinate Systems