Adaptive project scripts and analysis

Scripts and reports of the adaptive proton therapy project

To add a new patient from Jihun's data

There is more information in the README.md at patients/reports/README.md. Jihun has improved the data formats so this is what it is currently necessary:

• convertCBCTtofloat.sh: the code to transform the CBCTs to gPMC format is buggy, but works with floats :)
• maskSkin.sh: CAREFUL!! this script will destroy the original CBCTs, use with caution.
• re-createDicoms.sh: The dicom directory should be emptied beforehand.

To add a new patient plan:

• Create directory with patient number and ID in plans/Opt4D
• ./setMCAuto.sh with the directory in the main for loop (edit file or pass as parameter)
• Copy the patient directory (after having run MCAuto) to the cluster and create the Dijs per beam
• Link the Dijs in the Opt4D directory and create the structure.vv files in the local computer
• From ERISOne, send files (there is a script for that) to local computer
• Organize Opt4D files with _organizeOpt4DFiles.sh and _adjustWeights.sh
• ./setFractionsFiles.sh with the directory in the main for loop
• ./setGPUFiles.sh

To run a plan

The script runPatient.sh should run all the patients passed as parameters.