Polyquant CT reconstruction toolbox

Version 1.0.1 (91 MB) by Jonathan Mason

Toolbox for polyenergetic quantitative (polyquant) X-ray CT reconstruction with demos: including metal artifact and scatter correction.

https://github.com/cimentaur/polyquant

4.5

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Updated 2 Jun 2019

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# Polyquant CT Reconstruction Toolbox
This Matlab toolbox allows direct quantitative reconstruction from polyenergetic X-ray computed tomography (CT) measurements. We hope you find it useful and welcome any feedback or questions [j.mason@ed.ac.uk].

## Features
- Allows quantitative reconstruction into **electron density**, mass density, proton stopping power, quasi-monoenergetic and more.
- Iterative statistical reconstruction under Poisson noise.
- Metal artefact compensation and correction.
- Designed for use with [Michigan Image Reconstruction Toolbox](https://web.eecs.umich.edu/~fessler/code) operators: ensure the toolbox is in your path (by running its 'setup.m') before running these demos.
- Non-negative total variation (TV) reguarisation in 2D and 3D, adapted from [UNLocBoX](https://epfl-lts2.github.io/unlocbox-html/).
- Integrated polyenergetic scatter estimation and mitigation.
- Accelerated ordered sub-sets algorithm with bit-reversal ordering.

## Demos
We have included several demos to cover some of its functionality, including:
- 2D fanbeam CT reconstruction of brain, head, chest, abdomen and pelvis regions.
- 2D fanbeam CT metal artefact mitigation, from double titanium hip implants.
- 3D cone-beam CT reconstruction of head and pelvis regions, under 'full-fan' and 'half-fan' scans respectively.
- 3D cone-beam CT reconstruction with integrated polyenergetic scatter modelling (PolySKS).

## References
These methods are presented in the following publications (please cite if using):
- [Jonathan H Mason et al 2017 Phys. Med. Biol. 62 8739](https://doi.org/10.1088/1361-6560/aa9162)
- [Jonathan H Mason et al 2018 Phys. Med. Biol. 63 225001](https://doi.org/10.1088/1361-6560/aae794)

For more details, extensions and its use in radiotherapy, you can read the thesis:
[Quantitative cone-beam computed tomography reconstruction for radiotherapy planning](http://hdl.handle.net/1842/33193 )

## Acknowledgements
Thanks to Mike Davies, Bill Nailon and Alessandro Perelli for their collaboration and supervision during the development of this work. Another thanks to Alessandro for kindly reviewing this code.

Cite As

Jonathan Mason (2024). Polyquant CT reconstruction toolbox (https://github.com/cimentaur/polyquant), GitHub. Retrieved April 27, 2024.

Mason, Jonathan H., et al. “Polyquant CT: Direct Electron and Mass Density Reconstruction from a Single Polyenergetic Source.” Physics in Medicine and Biology, IOP Publishing, Oct. 2017, doi:10.1088/1361-6560/aa9162.

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Mason, Jonathan H., et al. “Quantitative Cone-Beam CT Reconstruction with Polyenergetic Scatter Model Fusion.” Physics in Medicine & Biology, vol. 63, no. 22, IOP Publishing, Nov. 2018, p. 225001, doi:10.1088/1361-6560/aae794.

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Version	Published	Release Notes
1.0.1	2 Jun 2019	updated description
1.0.0	31 May 2019

To view or report issues in this GitHub add-on, visit the GitHub Repository.

MLA	Mason, Jonathan H., et al. “Polyquant CT: Direct Electron and Mass Density Reconstruction from a Single Polyenergetic Source.” Physics in Medicine and Biology, IOP Publishing, Oct. 2017, doi:10.1088/1361-6560/aa9162.
APA	Mason, J. H., Perelli, A., Nailon, W. H., & Davies, M. E. (2017). Polyquant CT: direct electron and mass density reconstruction from a single polyenergetic source. Physics in Medicine and Biology. IOP Publishing. Retrieved from https://doi.org/10.1088%2F1361-6560%2Faa9162
BibTeX	@article{Mason_2017, doi = {10.1088/1361-6560/aa9162}, url = {https://doi.org/10.1088%2F1361-6560%2Faa9162}, year = 2017, month = {oct}, publisher = {{IOP} Publishing}, author = {Jonathan H Mason and Alessandro Perelli and William H Nailon and Mike E Davies}, title = {Polyquant {CT}: direct electron and mass density reconstruction from a single polyenergetic source}, journal = {Physics in Medicine and Biology} }

MLA	Mason, Jonathan H., et al. “Quantitative Cone-Beam CT Reconstruction with Polyenergetic Scatter Model Fusion.” Physics in Medicine & Biology, vol. 63, no. 22, IOP Publishing, Nov. 2018, p. 225001, doi:10.1088/1361-6560/aae794.
APA	Mason, J. H., Perelli, A., Nailon, W. H., & Davies, M. E. (2018). Quantitative cone-beam CT reconstruction with polyenergetic scatter model fusion. Physics in Medicine & Biology, 63(22), 225001. IOP Publishing. Retrieved from https://doi.org/10.1088%2F1361-6560%2Faae794
BibTeX	@article{Mason_2018, doi = {10.1088/1361-6560/aae794}, url = {https://doi.org/10.1088%2F1361-6560%2Faae794}, year = 2018, month = {nov}, publisher = {{IOP} Publishing}, volume = {63}, number = {22}, pages = {225001}, author = {Jonathan H Mason and Alessandro Perelli and William H Nailon and Mike E Davies}, title = {Quantitative cone-beam {CT} reconstruction with polyenergetic scatter model fusion}, journal = {Physics in Medicine {\&} Biology} }