Notes

Sensory Correlates associated with Interpersonal Area Leaks in the structure and suppleness within Autism Spectrum Condition.
Here we present an analysis protocol for dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) data of the kidneys. It covers comprehensive steps to facilitate signal to contrast agent concentration mapping via T1 mapping and the calculation of renal perfusion and filtration parametric maps using model-free approaches, model free analysis using deconvolution, the Toft's model and a Bayesian approach.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.Analysis of renal diffusion-weighted imaging (DWI) data to derive markers of tissue properties requires careful consideration of the type, extent, and limitations of the acquired data. Alongside data quality and general suitability for quantitative analysis, choice of diffusion model, fitting algorithm, and processing steps can have consequences for the precision, accuracy, and reliability of derived diffusion parameters. Here we introduce and discuss important steps for diffusion-weighted image processing, and in particular give example analysis protocols and pseudo-code for analysis using the apparent diffusion coefficient (ADC) and intravoxel incoherent motion (IVIM) models. Following an overview of general principles, we provide details of optional steps, and steps for validation of results. Illustrative examples are provided, together with extensive notes discussing wider context of individual steps, and notes on potential pitfalls.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 analysis protocol chapter is complemented by two separate chapters describing the basic concepts and experimental procedure.Renal hypoxia is generally accepted as a key pathophysiologic event in acute kidney injury of various origins and has also been suggested to play a role in the development of chronic kidney disease. Here we describe step-by-step data analysis protocols for MRI monitoring of renal oxygenation in rodents via the deoxyhemoglobin concentration sensitive MR parameters T2* and T2-a contrast mechanism known as the blood oxygenation level dependent (BOLD) effect.This chapter describes how to use the analysis tools provided by vendors of animal and clinical MR systems, as well as how to develop an analysis software. Aspects covered are data quality checks, data exclusion, model fitting, fitting algorithm, starting values, effects of multiecho imaging, and result validation.This chapter is based upon work from the PARENCHIMA COST Action, 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 is complemented by two separate chapters describing the basic concept and data analysis.The 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.In 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.Functional renal MRI promises access to a wide range of physiologically relevant parameters such as blood oxygenation, perfusion, tissue microstructure, pH, and sodium concentration. For quantitative comparison of results, representative values must be extracted from the parametric maps obtained with these different MRI techniques. To improve reproducibility of results this should be done based on regions-of-interest (ROIs) that are clearly and objectively defined.Semiautomated subsegmentation of the kidney in magnetic resonance images represents a simple but very valuable approach for the quantitative analysis of imaging parameters in multiple ROIs that are associated with specific anatomic locations. Thereby, it facilitates comparing MR parameters between different kidney regions, as well as tracking changes over time.Here we provide detailed step-by-step instructions for two recently developed subsegmentation techniques that are suitable for kidneys of small rodents i) the placement of ROIs in cortex, outer and the inner medulla based on typical kidney morphology and ii) the division of the kidney into concentrically oriented layers.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.Application of MRE for noninvasive evaluation of renal fibrosis has great potential for noninvasive assessment in patients with chronic kidney disease (CKD). CKD leads to severe complications, which require dialysis or kidney transplant and could even result in death. CKD in native kidneys and interstitial fibrosis in allograft kidneys are the two major kidney fibrotic pathologies where MRE may be clinically useful. Both these conditions can lead to extensive morbidity, mortality, and high health care costs. Currently, biopsy is the standard method for renal fibrosis staging. This method of diagnosis is painful, invasive, limited by sampling bias, exhibits inter- and intraobserver variability, requires prolonged hospitalization, poses risk of complications and significant bleeding, and could even lead to death. MRE based methods can potentially be useful to noninvasively detect, stage, and monitor renal fibrosis, reducing the need for renal biopsy. In this chapter, we describe experimental procedure and step by step instructions to run MRE along with some illustrative applications. We also includes sections on how to perform data quality check and analysis methods.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.Fluorinated compounds feature favorable toxicity profile and can be used as a contrast agent for magnetic resonance imaging and spectroscopy. Fluorine nucleus from fluorinated compounds exhibit well-known advantages of being a high signal nucleus with a natural abundance of its stable isotope, a convenient gyromagnetic ratio close to that of protons, and a unique spectral signature with no detectable background at clinical field strengths. Perfluorocarbon core nanoparticles (PFC NP) are a class of clinically approved emulsion agents recently applied in vivo for ligand-targeted molecular imaging. The objective of this chapter is to outline a multinuclear 1H/19F MRI protocol for functional kidney imaging in rodents for mapping of renal blood volume and oxygenation (pO2) in renal disease 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 experimental protocol chapter is complemented by a separate chapter describing the basic concept of functional imaging using fluorine (19F) MR methods.Inflammation is one underlying contributing factor in the pathology of acute and chronic kidney disorders. Phagocytes such as monocytes, neutrophils and dendritic cells are considered to play a deleterious role in the progression of kidney disease but may also contribute to organ homeostasis. The kidney is a target of life-threatening autoimmune disorders such as the antineutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV). Neutrophils and monocytes express ANCA antigens and play an important role in the pathogenesis of AAV. Noninvasive in vivo methods that can quantify the distribution of inflammatory cells in the kidney as well as other organs in vivo would be vital to identify the causality and significance of inflammation during disease progression. Here we describe an noninvasive technique to study renal inflammation in rodents in vivo using fluorine (19F) MRI. In this protocol we chose a murine ANCA-AAV model of renal inflammation and made use of nanoparticles prepared from perfluoro-5-crown-15-ether (PFCE) for renal 19F 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 is complemented by two separate chapters describing the basic concept and data analysis.Alterations in renal metabolism are associated with both physiological and pathophysiologic events. The existing noninvasive analytic tools including medical imaging have limited capability for investigating these processes, which potentially limits current understanding of kidney disease and the precision of its clinical diagnosis. Hyperpolarized 13C MRI is a new medical imaging modality that can capture changes in the metabolic processing of certain rapidly metabolized substrates, as well as changes in kidney function. Here we describe experimental protocols for renal metabolic [1-13C]pyruvate and functional 13C-urea imaging step-by-step. These methods and protocols are useful for investigating renal blood flow and function as well as the renal metabolic status of rodents in vivo under various experimental (patho)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.
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