Sue edits

paper/paper.md

@@ -51,11 +51,11 @@ The layer image and quantitative images are resampled to the same spatial resolu
 An object-oriented interface is provided to allow end users to simply generate layers and apply these to qMR images. [Documentation](https://qlayers.readthedocs.io/) is provided to guide users through installation via `PyPI`, `conda` or from [source code on GitHub](https://github.com/alexdaniel654/qlayers); it also includes tutorials and an API reference. An automated test suite with high coverage provides users with confidence in the stability of `3DQLayers` and that there will be no unexpected changes to results unless highlighted in the change-log.
 
 ## Usage Examples
-\autoref{fig:egfr_gradients} shows the use of `3DQLayers` to measure different gradients of R~2~^\*^ in a heathy volunteer with normal renal function and a patient with impaired renal function (an estimated glomerular filtration rate (eGFR) of above 90 ml/min/1.73m^2^ measured from blood samples is considered in the healthy range [@stevens_assessing_2006]). This replicates results shown using TLCO, with a lower gradient in patients compared to healthies, however `3DQLayers` controls for kidney size resulting in the gradient being measured in quantitative units of Hz/mm rather than Hz/layer as in TLCO, thus increasing generalisability.
+\autoref{fig:egfr_gradients} shows the application of `3DQLayers` to measure different gradients of the transverse relaxation rate R~2~^\*^ in a heathy volunteer with normal renal function and a patient with impaired renal function (an estimated glomerular filtration rate (eGFR) of above 90 ml/min/1.73m^2^ measured from blood samples is considered in the healthy range [@stevens_assessing_2006]). This replicates results shown using TLCO, with a lower gradient in patients compared to healthies, however `3DQLayers` controls for kidney size resulting in the gradient being measured in quantitative units of Hz/mm rather than Hz/layer as in TLCO, thus increasing generalisability.
 
 \autoref{fig:cortical_thickness} shows how `3DQLayers` can be used in combination with cortex and medulla tissue ROIs to analyse the distribution of voxel counts of each tissue as a function of layer depth of the kidney. Here cortex and medulla ROIs are initially generated using a Gaussian mixture model to segment a T~1~-weighted structural image followed by manual ROI correction. From this, average renal cortical thickness can be defined from the depth at which the voxel distribution crosses from cortex to medulla. Cortical thickness has been hypothesised as a potential biomarker of renal disease [@yamashita_value_2015; @korkmaz_clinical_2017]. 
 
-`3DQLayers` can also be used to analyse *ex-vivo* kidneys imaged outside the body. \autoref{fig:exvivo_profiles} shows example quantitative maps acquired from a kidney removed for transplant but subsequently deemed unsuitable and the associated layer profiles. \autoref{fig:roi_layers_corr} compares the results of tissue ROI based analysis and layer-based analysis in fifteen transplant kidneys. A significant correlation between outer layers and the cortex, and inner layers and the medulla was shown across all quantitative mapping techniques and a significant correlation between cortico-medullary ratio and layer gradient was shown for T~1~, T~2~, T~2~ ^\*^ and Magnetisation Transfer Ratio (MTR) mapping.
+`3DQLayers` can also be used to analyse *ex-vivo* kidneys imaged outside the body. \autoref{fig:exvivo_profiles} shows example quantitative maps acquired from a kidney retrieved for transplant but subsequently deemed unsuitable and the associated layer profiles. \autoref{fig:roi_layers_corr} compares the results of tissue ROI based analysis and layer-based analysis in fifteen transplant kidneys. A significant correlation between outer layers and the cortex, and inner layers and the medulla was shown across all quantitative mapping techniques and a significant correlation between cortico-medullary ratio and layer gradient was shown for T~1~, T~2~, T~2~ ^\*^ and Magnetisation Transfer Ratio (MTR) mapping.
 
 # Figures
 ![a) A schematic of the kidneys showing the renal cortex and medullary pyramids. b) A T~1~-weighted structural MR image of the abdomen showing the kidneys with the renal cortex appearing as a light band on the outer edge of the kidney and the medullary pyramids as darker patches on the inner portion of the kidneys. \label{fig:renal_structure}](kidney_overview.png){ width=90% }