python and ITK-Based workflow to generate pseudo-Xray

If interested to run the scripts here, change all directories to your local directories (for all bash script.. i believe...)

This set of scripts will need python modules: (1)dicom2nifit, (2)dipy, (3)pydicom, (4)nibbabel and ITK (only needed for creating synthetic xray)

To convert series of dicom images into 3D, interpolated, nifti volume, run:

./extractNifti.sh <Start index> <End index> (note: index are patient id)

To create synthetic xray / DRR from the CT volume generated above, run:

./runDrive.sh <Start index> <End index> 

Building ITK : (quick build ITK: https://itk.org/Wiki/ITK/Getting_Started/Build/Linux ; complete software guide of ITK: https://itk.org/ItkSoftwareGuide.pdf)