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Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function

There is a growing demand for fast, accurate computation of clinical markers to improve renal function and anatomy assessment with a single study. However, conventional techniques have limitations leading to overestimations of kidney function or failure to provide sufficient spatial resolution to ta...

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Autores principales: Asaturyan, Hykoush, Villarini, Barbara, Sarao, Karen, Chow, Jeanne S., Afacan, Onur, Kurugol, Sila
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8659486/
https://www.ncbi.nlm.nih.gov/pubmed/34883946
http://dx.doi.org/10.3390/s21237942
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author Asaturyan, Hykoush
Villarini, Barbara
Sarao, Karen
Chow, Jeanne S.
Afacan, Onur
Kurugol, Sila
author_facet Asaturyan, Hykoush
Villarini, Barbara
Sarao, Karen
Chow, Jeanne S.
Afacan, Onur
Kurugol, Sila
author_sort Asaturyan, Hykoush
collection PubMed
description There is a growing demand for fast, accurate computation of clinical markers to improve renal function and anatomy assessment with a single study. However, conventional techniques have limitations leading to overestimations of kidney function or failure to provide sufficient spatial resolution to target the disease location. In contrast, the computer-aided analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) could generate significant markers, including the glomerular filtration rate (GFR) and time–intensity curves of the cortex and medulla for determining obstruction in the urinary tract. This paper presents a dual-stage fully modular framework for automatic renal compartment segmentation in 4D DCE-MRI volumes. (1) Memory-efficient 3D deep learning is integrated to localise each kidney by harnessing residual convolutional neural networks for improved convergence; segmentation is performed by efficiently learning spatial–temporal information coupled with boundary-preserving fully convolutional dense nets. (2) Renal contextual information is enhanced via non-linear transformation to segment the cortex and medulla. The proposed framework is evaluated on a paediatric dataset containing 60 4D DCE-MRI volumes exhibiting varying conditions affecting kidney function. Our technique outperforms a state-of-the-art approach based on a GrabCut and support vector machine classifier in mean dice similarity (DSC) by 3.8% and demonstrates higher statistical stability with lower standard deviation by 12.4% and 15.7% for cortex and medulla segmentation, respectively.
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spelling pubmed-86594862021-12-10 Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function Asaturyan, Hykoush Villarini, Barbara Sarao, Karen Chow, Jeanne S. Afacan, Onur Kurugol, Sila Sensors (Basel) Article There is a growing demand for fast, accurate computation of clinical markers to improve renal function and anatomy assessment with a single study. However, conventional techniques have limitations leading to overestimations of kidney function or failure to provide sufficient spatial resolution to target the disease location. In contrast, the computer-aided analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) could generate significant markers, including the glomerular filtration rate (GFR) and time–intensity curves of the cortex and medulla for determining obstruction in the urinary tract. This paper presents a dual-stage fully modular framework for automatic renal compartment segmentation in 4D DCE-MRI volumes. (1) Memory-efficient 3D deep learning is integrated to localise each kidney by harnessing residual convolutional neural networks for improved convergence; segmentation is performed by efficiently learning spatial–temporal information coupled with boundary-preserving fully convolutional dense nets. (2) Renal contextual information is enhanced via non-linear transformation to segment the cortex and medulla. The proposed framework is evaluated on a paediatric dataset containing 60 4D DCE-MRI volumes exhibiting varying conditions affecting kidney function. Our technique outperforms a state-of-the-art approach based on a GrabCut and support vector machine classifier in mean dice similarity (DSC) by 3.8% and demonstrates higher statistical stability with lower standard deviation by 12.4% and 15.7% for cortex and medulla segmentation, respectively. MDPI 2021-11-28 /pmc/articles/PMC8659486/ /pubmed/34883946 http://dx.doi.org/10.3390/s21237942 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Asaturyan, Hykoush
Villarini, Barbara
Sarao, Karen
Chow, Jeanne S.
Afacan, Onur
Kurugol, Sila
Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function
title Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function
title_full Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function
title_fullStr Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function
title_full_unstemmed Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function
title_short Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function
title_sort improving automatic renal segmentation in clinically normal and abnormal paediatric dce-mri via contrast maximisation and convolutional networks for computing markers of kidney function
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8659486/
https://www.ncbi.nlm.nih.gov/pubmed/34883946
http://dx.doi.org/10.3390/s21237942
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