scholarly journals Denoising for Improved Parametric MRI of the Kidney: Protocol for Nonlocal Means Filtering

2021 ◽  
pp. 565-576
Author(s):  
Ludger Starke ◽  
Karsten Tabelow ◽  
Thoralf Niendorf ◽  
Andreas Pohlmann
Keyword(s):  
Relaxation Times ◽  
The European Union ◽  
Noise Component ◽  
Nonlocal Means ◽  
Low Snr ◽  
European Cooperation ◽  
Single Voxel ◽  
Renal Mri ◽  
The Cost ◽  
Spatial Patches

AbstractIn order to tackle the challenges caused by the variability in estimated MRI parameters (e.g., T2* and T2) due to low SNR a number of strategies can be followed. One approach is postprocessing of the acquired data with a filter. The basic idea is that MR images possess a local spatial structure that is characterized by equal, or at least similar, noise-free signal values in vicinities of a location. Then, local averaging of the signal reduces the noise component of the signal. In contrast, nonlocal means filtering defines the weights for averaging not only within the local vicinity, bur it compares the image intensities between all voxels to define “nonlocal” weights. Furthermore, it generally compares not only single-voxel intensities but small spatial patches of the data to better account for extended similar patterns. Here we describe how to use an open source NLM filter tool to denoise 2D MR image series of the kidney used for parametric mapping of the relaxation times T2* and T2.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.

scholarly journals Recommendations for Preclinical Renal MRI: A Comprehensive Open-Access Protocol Collection to Improve Training, Reproducibility, and Comparability of Studies

2021 ◽  
pp. 3-23
Author(s):  
Andreas Pohlmann ◽  
Susan J. Back ◽  
Andrea Fekete ◽  
Iris Friedli ◽  
Stefanie Hectors ◽  
...  
Keyword(s):  
Routine Clinical Practice ◽  
Small Animals ◽  
The European Union ◽  
European Cooperation ◽  
Comprehensive Collection ◽  
Mri Studies ◽  
Quantum Leap ◽  
Renal Mri ◽  
The Cost ◽  
Crucial Part

AbstractRenal MRI holds incredible promise for making a quantum leap in improving diagnosis and care of patients with a multitude of diseases, by moving beyond the limitations and restrictions of current routine clinical practice. Clinical and preclinical renal MRI is advancing with ever increasing rapidity, and yet, aside from a few examples of renal MRI in routine use, it is still not good enough. Several roadblocks are still delaying the pace of progress, particularly inefficient education of renal MR researchers, and lack of harmonization of approaches that limits the sharing of results among multiple research groups.Here we aim to address these limitations for preclinical renal MRI (predominantly in small animals), by providing a comprehensive collection of more than 40 publications that will serve as a foundational resource for preclinical renal MRI studies. This includes chapters describing the fundamental principles underlying a variety of renal MRI methods, step-by-step protocols for executing renal MRI studies, and detailed guides for data analysis. This collection will serve as a crucial part of a roadmap toward conducting renal MRI studies in a robust and reproducible way, that will promote the standardization and sharing of data.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.

scholarly journals Experimental Protocols for MRI Mapping of Renal T1

2021 ◽  
pp. 383-402
Author(s):  
Philippe Garteiser ◽  
Octavia Bane ◽  
Sabrina Doblas ◽  
Iris Friedli ◽  
Stefanie Hectors ◽  
...  
Keyword(s):  
Small Animal ◽  
Water Proton ◽  
The European Union ◽  
Imaging Protocol ◽  
European Cooperation ◽  
Experimental Protocols ◽  
Renal Mri ◽  
Kidney Imaging ◽  
The Cost ◽  
Clinical Scanner

AbstractThe water proton longitudinal relaxation time, T1, is a common and useful MR parameter in nephrology research. Here we provide three step-by-step T1-mapping protocols suitable for different types of nephrology research. Firstly, we provide a single-slice 2D saturation recovery protocol suitable for studies of global pathology, where whole-kidney coverage is unnecessary. Secondly, we provide an inversion recovery type imaging protocol that may be optimized for specific kidney disease applications. Finally, we also provide imaging protocol for small animal kidney imaging in a clinical scanner.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure.

scholarly journals MRI Mapping of Renal T1: Basic Concept

2021 ◽  
pp. 157-169
Author(s):  
Stefanie J. Hectors ◽  
Philippe Garteiser ◽  
Sabrina Doblas ◽  
Gwenaël Pagé ◽  
Bernard E. Van Beers ◽  
...  
Keyword(s):  
European Union ◽  
Basic Concept ◽  
Measurement Techniques ◽  
The European Union ◽  
Experimental Procedure ◽  
Tissue Microenvironment ◽  
European Cooperation ◽  
Renal Mri ◽  
The Cost ◽  
Substantial Interest

AbstractIn renal MRI, measurement of the T1 relaxation time of water molecules may provide a valuable biomarker for a variety of pathological conditions. Due to its sensitivity to the tissue microenvironment, T1 has gained substantial interest for noninvasive imaging of renal pathology, including inflammation and fibrosis. In this chapter, we will discuss the basic concept of T1 mapping and different T1 measurement techniques and we will provide an overview of emerging preclinical applications of T1 for imaging of kidney disease.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This introduction chapter is complemented by two separate chapters describing the experimental procedure and data analysis.

scholarly journals Essential Practical Steps for MRI of the Kidney in Experimental Research

2021 ◽  
pp. 349-367
Author(s):  
Andreas Pohlmann ◽  
João S. Periquito ◽  
Thoralf Niendorf
Keyword(s):  
Structural Information ◽  
Imaging Techniques ◽  
The European Union ◽  
European Cooperation ◽  
Slice Orientation ◽  
Magnetic Resonance Imaging Mri ◽  
Preclinical Mri ◽  
Renal Mri ◽  
And Function ◽  
The Cost

AbstractMagnetic resonance imaging (MRI) is an emerging method to obtain valuable functional and structural information about the kidney noninvasively. Before performing specialized MR measurements for probing tissue structure and function, some essential practical steps are needed, which are common for most applications. Here we describe in a step-by-step manner how to (1) achieve the double-oblique slice orientation coronal-to-the-kidney, (2) adapt the scan protocol for avoiding aortic flow artifacts and covering both kidneys, (3) perform localized shimming on the kidney, and (4) check perfusion in the large renal blood vessels using time-of-flight (TOF) angiography. The procedures are tailored to preclinical MRI but conceptionally are also applicable to human MRI.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This experimental protocol chapter explains the initial and essential MRI steps that precede specific functional and structural MR imaging techniques (T1- and T2*-mapping, DWI, ASL, etc.), which are described in separate chapters.

scholarly journals Analysis Protocols for MRI Mapping of Renal T1

2021 ◽  
pp. 577-590
Author(s):  
Philippe Garteiser ◽  
Gwenaël Pagé ◽  
Sabrina Doblas ◽  
Octavia Bane ◽  
Stefanie Hectors ◽  
...  
Keyword(s):  
Software Requirements ◽  
Small Animals ◽  
The European Union ◽  
Experimental Procedure ◽  
European Cooperation ◽  
Precise Characterization ◽  
Renal Mri ◽  
The Cost ◽  
Analysis Protocol

AbstractThe computation of T1 maps from MR datasets represents an important step toward the precise characterization of kidney disease models in small animals. Here the main strategies to analyze renal T1 mapping datasets derived from small rodents are presented. Suggestions are provided with respect to essential software requirements, and advice is provided as to how dataset completeness and quality may be evaluated. The various fitting models applicable to T1 mapping are presented and discussed. Finally, some methods are proposed for validating the obtained results.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure.

scholarly journals Functional Imaging Using Fluorine (19F) MR Methods: Basic Concepts

2021 ◽  
pp. 279-299
Author(s):  
Sonia Waiczies ◽  
Christian Prinz ◽  
Ludger Starke ◽  
Jason M. Millward ◽  
Paula Ramos Delgado ◽  
...  
Keyword(s):  
Renal Function ◽  
The European Union ◽  
Functional Changes ◽  
European Cooperation ◽  
Disease States ◽  
Signal Sensitivity ◽  
Renal Mri ◽  
The Cost ◽  
New Applications

AbstractKidney-associated pathologies would greatly benefit from noninvasive and robust methods that can objectively quantify changes in renal function. In the past years there has been a growing incentive to develop new applications for fluorine (19F) MRI in biomedical research to study functional changes during disease states. 19F MRI represents an instrumental tool for the quantification of exogenous 19F substances in vivo. One of the major benefits of 19F MRI is that fluorine in its organic form is absent in eukaryotic cells. Therefore, the introduction of exogenous 19F signals in vivo will yield background-free images, thus providing highly selective detection with absolute specificity in vivo. Here we introduce the concept of 19F MRI, describe existing challenges, especially those pertaining to signal sensitivity, and give an overview of preclinical applications to illustrate the utility and applicability of this technique for measuring renal function in animal models.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This introduction chapter is complemented by two separate chapters describing the experimental procedure and data analysis.

scholarly journals Preparation and Monitoring of Small Animals in Renal MRI

2021 ◽  
pp. 45-55
Author(s):  
Tamas Kaucsar ◽  
Adam Hosszu ◽  
Erdmann Seeliger ◽  
Henning M. Reimann ◽  
Andrea Fekete
Keyword(s):  
Therapeutic Strategies ◽  
Renal Diseases ◽  
Small Animals ◽  
The European Union ◽  
Mortality And Morbidity ◽  
Surgical Interventions ◽  
European Cooperation ◽  
Magnetic Resonance Imaging Mri ◽  
Renal Mri ◽  
The Cost

AbstractRenal diseases remain devastating illnesses with unacceptably high rates of mortality and morbidity worldwide. Animal models are essential tools to better understand the pathomechanism of kidney-related illnesses and to develop new, successful therapeutic strategies. Magnetic resonance imaging (MRI) has been actively explored in the last decades for assessing renal function, perfusion, tissue oxygenation as well as the degree of fibrosis and inflammation. This chapter aims to provide an overview of the preparation and monitoring of small animals before, during, and after surgical interventions or MR imaging. Standardization of experimental settings such as body temperature or hydration of animals and minimizing pain and distress are essential for diminishing nonexperimental variables as well as for conducting ethical research.This publication is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers.

scholarly journals Analysis Methods for Hyperpolarized Carbon (13C) MRI of the Kidney

2021 ◽  
pp. 697-710
Author(s):  
Galen D. Reed ◽  
Natalie J. Korn ◽  
Christoffer Laustsen ◽  
Cornelius von Morze
Keyword(s):  
Imaging Modality ◽  
Functional Information ◽  
The European Union ◽  
Experimental Procedure ◽  
European Cooperation ◽  
Renal Mri ◽  
And Function ◽  
The Cost ◽  
Analysis Protocol

AbstractHyperpolarized 13C MR is a novel medical imaging modality with substantially different signal dynamics as compared to conventional 1H MR, thus requiring new methods for processing the data in order to access and quantify the embedded metabolic and functional information. Here we describe step-by-step analysis protocols for functional renal hyperpolarized 13C imaging. These methods are useful for investigating renal blood flow and function as well as metabolic status of rodents in vivo under various experimental physiological conditions.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure.

scholarly journals Analysis Protocol for Renal Sodium (23Na) MR Imaging

2021 ◽  
pp. 689-696
Author(s):  
James T. Grist ◽  
Esben Søvsø Szocska Hansen ◽  
Frank G. Zöllner ◽  
Christoffer Laustsen
Keyword(s):  
Mr Imaging ◽  
The European Union ◽  
Simple Task ◽  
European Cooperation ◽  
Concentration Estimation ◽  
Sodium Gradient ◽  
Quadrupolar Relaxation ◽  
Renal Mri ◽  
The Cost ◽  
Analysis Protocol

AbstractThe signal acquired in sodium (23Na) MR imaging is proportional to the concentration of sodium in a voxel, and it is possible to convert between the two using external calibration phantoms. Postprocessing, and subsequent analysis, of sodium renal images is a simple task that can be performed with readily available software. Here we describe the process of conversion between sodium signal and concentration, estimation of the corticomedullary sodium gradient and the procedure used for quadrupolar relaxation analysis.This chapter is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This analysis protocol chapter is complemented by two separate chapters describing the basic concept and experimental procedure.

scholarly journals Hardware Considerations for Preclinical Magnetic Resonance of the Kidney

2021 ◽  
pp. 131-155
Author(s):  
Paula Ramos Delgado ◽  
Ekkehard Küstermann ◽  
André Kühne ◽  
Jason M. Millward ◽  
Thoralf Niendorf ◽  
...  
Keyword(s):  
Magnetic Resonance ◽  
Small Animals ◽  
The European Union ◽  
European Cooperation ◽  
Competing Demands ◽  
Magnetic Resonance Imaging Mri ◽  
Preclinical Mri ◽  
Renal Mri ◽  
The Cost ◽  
Imaging Speed

AbstractMagnetic resonance imaging (MRI) is a noninvasive imaging technology that offers unparalleled anatomical and functional detail, along with diagnostic sensitivity. MRI is suitable for longitudinal studies due to the lack of exposure to ionizing radiation. Before undertaking preclinical MRI investigations of the kidney, the appropriate MRI hardware should be carefully chosen to balance the competing demands of image quality, spatial resolution, and imaging speed, tailored to the specific scientific objectives of the investigation. Here we describe the equipment needed to perform renal MRI in rodents, with the aim to guide the appropriate hardware selection to meet the needs of renal MRI applications.This publication is based upon work from the COST Action PARENCHIMA, a community-driven network funded by the European Cooperation in Science and Technology (COST) program of the European Union, which aims to improve the reproducibility and standardization of renal MRI biomarkers. This chapter on hardware considerations for renal MRI in small animals is complemented by two separate publications describing the experimental procedure and data analysis.

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