This is the repository for the 4D Cone Beam CT Image quality and parameter optimizing Project. Carleton University Physics 2018. Supervisors: A.Elsayed, E.Heath, T.Xu
Sample data can be found at: sftp://tyr.physics.carleton.ca/data/data068/mwaqar/Sample%20Data/img_1.3.46.423632.1354522017101323295146.75%20copy.zip The Sample data contains a 4DCBCT Scan of CIRM Dynamic phantom in Cos^4 motion with a phase time of 4 seconds and tumour travel of 20mm.
This project uses tools from the Reconstruction Tool Kit (RTK) consortium. To install it on a Linux based system run Auto-RTK-ITK-VTK-Install.sh This will also install the Insight Segmentation and Registration Toolkit (ITK) and Visualization Toolkit (VTK)
Before running it assure that the following tools are installed on your system:
- GIT
- CMake
- C/C++ Compiler
To install these on a mac simply run the following spinets in terminal:
#installing homebrew
/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
#Installing GIT
brew install git
#Installing CMake
brew install cmake
The code uses CBCT scans from the Elekta XVI v.5 system. These files should contain the following:
- *.HIS files
- location: \DICOMID (ie. img_1.3.46.423632.1354522017101323295146.75)
- _FRAMES.XML file
- location: \DICOMID
- *.SORT.txt file
- location: \DICOMID\Reconstruction (ie. img_1.3.46.423632.1354522017101323295146.75\Reconstruction)
The data should be processed in the following order:
-
Resorting (binning) using 4DCBCT-Resort-XMLgen.py:
This code will read in the *.HIS file, XML file, and the *.SORT.txt file. It outputs sorted/binned *.HIS and new XML files
-
Reconstructing each phase using 4D-Recon-script
Inputs: Location of the RTK Compiled code (ie. it's binary) and SCAN DICOMID Output: 10 reconstruction (one for each phase) location is set by RtkGeoOutLoc