How to use the software

Regular reconstruction, registration and scatter correction

The following list will guide you through how to do a complete CB scatter correction.

1. open the directory containing the projection data, i.e. *.hnd, *.xim, *.xvi
2. If elekta projections open a geometry file (generated from RTK)
3. Press LOAD and answer the prompts on screen (skip to 7. if the planCT was loaded and immediate reconstruction was chosen)
4. Do Beam hardening and bowtie correction of projections if necessary.
5. Load Plan CT, from DICOM folder or mha file.
6. In the view menu select Registration.
7. Set Fixed Image to RAW_CBCT and Moving Image to MANUAL_CT
8. Check Keyboard and use the arrow keys + PageUp and PageDown to do a rough rigid registration.
9. Optional: Press Gradient, to let plastimatch improve the MANUAL_CT registration
10. Press Do registration in the "Plastimatch-rigid body" box to let plastimatch do the final rigid registration and set the image size and resolution to that of the RAW_CBCT.
11. Press Do registration in the "Plastimatch-deformable" box, (optionally change the values and add steps first).
12. If you are happy with the deformable registration, proceed to 13. otherwise set Moving Image to AUTO_RIGID_CT and go back to 11. and do the optional part.
13. Back in the main window, press Correct to do the scatter correction.
14. If you are happy, you can export the files from the file menu. Otherwise, press ReLoad Proj., change some settings, make sure Moving Image is DEFORMED_CT_FINAL, and try again.

Other features/settings

There are a lot of features and settings in the program. I recommend loading some data and then just clicking on everything, play around, see what happens. In most cases the standard output will explain what happened or what didn't.