RTK/Examples/MCCBCTReconstruction

RTK provides the necessary tools to reconstruct an image with motion compensation. The implementation is based on two articles that we have published (article 1 and article 2) but only the FDK-based motion-compensated CBCT reconstruction (analytic algorithm in article 1) and without optimization (very slow reconstruction compared to article 2). You should read the articles to understand the basics of the algorithm before trying to use the software.

The algorithm requires a set of projection images with the associated RTK geometry, the respiratory phase of each projection image and the 4D motion vector field over a respiratory cycle in the cone-beam coordinate system. Each piece of data is described in more details below. It is assumed that we have a breathing motion that is cyclic and similar to that described by the vector field. Note that you could modify the code and create your own motion model if you want to, in which case you should probably contact us.

Projection images

This example is illustrated with a set of projection images of the POPI patient. This dataset has been used in the first previously-mentioned article. You can download the projections and the required tables of the Elekta database, FRAME.DBF and IMAGE.DBF, from MIDAS. The dataset is first used to reconstruct a blurry image:

# Convert Elekta database to RTK geometry
rtkelektasynergygeometry \
  -o geometry.rtk \
  -f FRAME.DBF \
  -i IMAGE.DBF \
  -u 1.3.46.423632.141000.1169042526.68

# Reconstruct from all projection images without any motion compensation
rtkfdk \
  -p . \
  -r .*.his \
  -o fdk.mha \
  -g geometry.rtk \
  --hann 0.5 \
  --pad 1.0

# Keep only the field-of-view of the image
rtkfieldofview \
  --reconstruction fdk.mha \
  --output fdk.mha \
  --geometry geometry.rtk \
  --path . \
  --regexp '.*.his'

You should obtain something like that with VV:

Deformation vector field

The next piece of data is a 4D deformation vector field that describes a respiratory cycle. Typically, it can be obtained from the 4D planning CT.