Bibliography

Here are a few of the resources that this project either builds on or makes heavy use of. Additionally, there are a few alternative pieces of software that are similar to this project that may be of interest to the reader.

Papers

Twelve Layer Concentric Objects (TLCO) method

  • Piskunowicz M, Hofmann L, Zuercher E, et al. A new technique with high reproducibility to estimate renal oxygenation using BOLD-MRI in chronic kidney disease. Magn Reson Imaging. 2015;33(3):253-261. doi:10.1016/j.mri.2014.12.002

  • Milani B, Ansaloni A, Sousa-Guimaraes S, et al. Reduction of cortical oxygenation in chronic kidney disease: evidence obtained with a new analysis method of blood oxygenation level-dependent magnetic resonance imaging. Nephrol Dial Transplant. 2017;32(12):2097-2105. doi:10.1093/ndt/gfw362

  • Pruijm M, Milani B, Pivin E, et al. Reduced cortical oxygenation predicts a progressive decline of renal function in patients with chronic kidney disease. Kidney Int. 2018;93(4):932-940. doi:10.1016/j.kint.2017.10.020

  • Li LP, Milani B, Pruijm M, et al. Renal BOLD MRI in patients with chronic kidney disease: comparison of the semi-automated twelve layer concentric objects (TLCO) and manual ROI methods. Magn Reson Mater Phys Biol Med. 2020;33(1):113-120. doi:10.1007/s10334-019-00808-5

Automated Kidney Segmentation

  • Daniel AJ, Buchanan CE, Allcock T, et al. Automated renal segmentation in healthy and chronic kidney disease subjects using a convolutional neural network. Magnetic Resonance in Medicine. 2021;86(2):1125-1136. doi:10.1002/mrm.28768

Software

  • Trimesh - A library for interacting with meshes in Python.

  • Renal Segmentor - Automated kidneys segmentation from T2-weighted FSE images using a convolutional neural network.

  • UKAT - UK Renal Imaging Network Kidney Analysis Toolbox, a framework for generating quantitative maps from renal MRI data.

  • LAYNII - One of the more popular tools for layer analysis of the brain.