This project contains a part of the code useful to reproduce the image processing pipeline proposed in the article by Maspero M. et al, Phys Med Biol (2017)62. The article presents an approach to disentangle confounding factor that may occur in dose comparison study for the evaluation of Magnetic Resonance (MR)-only based radiotherapy treatment planning.
We proposed a strategy to circumvent inter-scan differences between Computer Tomography (CT) and MR imaging session by generating CT-based pseudo-CT (pCT) that mimic the output of the pCT generation method used in our clinic.
A simplified version of the code used to generate MR- and CT based pCT. The code here presented illustrates how to: 1. access to dicom data; 2. automatically delineate the CT body contour; 3. generate water-equivalent bulk-assigned pCT; 4. generate pCT that mimic the bulk-assignment proposed by the MR-based pCT generation method used in the article; 5. properly generate pCT that can be pushed to a database, maintaining the relation with the original data.
Run the code? Simply clone/download the repository and run ImagePreparation_pCTgen.m within Matlab. Note that the code has been developed and benchmarked in Matlab R2015a and we do not ensure/support workability for different versions of Matlab.
Run the code without downloading anything? Go to Ocean Code share capsule https://codeocean.com/2017/10/27/mri-only-proton-colon-bulk-assigned-pseudo-ct-images-generation-with-air/ and simply click run and wait about 1.5 min to get the output. You will also be able to inspect the code and directly work there!
Maspero Matteo (@matteomaspero), PhD candidate at University Medical Center Utrecht, The Netherlands. In case you are using any of the material, please refer to the article. The link is : http://dx.doi.org/10.1088/1361-6560/aa4fe7
Do you have any question about the methods, or are you having trouble with the page? Please contact the owner of the repository & thank you very much in advance for any comments.